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Created 2015-05-07 09:22:47 | Updated 2015-05-07 10:09:41 | Tags: haplotypecaller format genotypegvcfs info-field
Comments (18)

I have a potential bug running GATK GenotypeGVCFs. It complains that there is a DP in the INFO field, but in my haplotypecaller-generated -mg.g.vcf.gz's I do not have a DP in the info, I do have DP in the FORMAT field though, but that's present in the headers as shown below the error output.

Any idea what could be the problem?

INFO  18:30:12,694 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  18:30:12,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-geee94ec, Compiled 2015/03/09 14:27:22 
INFO  18:30:12,699 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  18:30:12,699 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  18:30:12,706 HelpFormatter - Program Args: -l INFO -T GenotypeGVCFs -R /net/NGSanalysis/ref/Mus_musculus.GRCm38/index/bwa/Mus_musculus.GRCm38.dna.primary_assembly.fa -o /dev/stdout -ploidy 2 --num_threads 32 --intervals:targets,BED /net/NGSanalysis/ref/Mus_musculus.GRCm38/bed/SeqCap/ex100/110624_MM10_exome_L2R_D02_EZ_HX1-ex100.bed --max_alternate_alleles 20 -V:3428_10_14_SRO_185_TGGCTTCA-mg,VCF 3428_10_14_SRO_185_TGGCTTCA-mg.g.vcf.gz -V:3428_11_14_SRO_186_TGGTGGTA-mg,VCF 3428_11_14_SRO_186_TGGTGGTA-mg.g.vcf.gz -V:3428_12_13_SRO_422_TTCACGCA-mg,VCF 3428_12_13_SRO_422_TTCACGCA-mg.g.vcf.gz -V:3428_13_13_SRO_492_AACTCACC-mg,VCF 3428_13_13_SRO_492_AACTCACC-mg.g.vcf.gz -V:3428_14_13_SRO_493_AAGAGATC-mg,VCF 3428_14_13_SRO_493_AAGAGATC-mg.g.vcf.gz -V:3428_15_14_SRO_209_AAGGACAC-mg,VCF 3428_15_14_SRO_209_AAGGACAC-mg.g.vcf.gz -V:3428_16_14_SRO_218_AATCCGTC-mg,VCF 3428_16_14_SRO_218_AATCCGTC-mg.g.vcf.gz -V:3428_17_14_SRO_201_AATGTTGC-mg,VCF 3428_17_14_SRO_201_AATGTTGC-mg.g.vcf.gz -V:3428_18_13_SRO_416_ACACGACC-mg,VCF 3428_18_13_SRO_416_ACACGACC-mg.g.vcf.gz -V:3428_19_14_SRO_66_ACAGATTC-mg,VCF 3428_19_14_SRO_66_ACAGATTC-mg.g.vcf.gz -V:3428_1_13_SRO_388_GTCGTAGA-mg,VCF 3428_1_13_SRO_388_GTCGTAGA-mg.g.vcf.gz -V:3428_20_14_SRO_68_AGATGTAC-mg,VCF 3428_20_14_SRO_68_AGATGTAC-mg.g.vcf.gz -V:3428_21_14_SRO_210_AGCACCTC-mg,VCF 3428_21_14_SRO_210_AGCACCTC-mg.g.vcf.gz -V:3428_22_14_SRO_256_AGCCATGC-mg,VCF 3428_22_14_SRO_256_AGCCATGC-mg.g.vcf.gz -V:3428_23_14_SRO_270_AGGCTAAC-mg,VCF 3428_23_14_SRO_270_AGGCTAAC-mg.g.vcf.gz -V:3428_24_13_SRO_452_ATAGCGAC-mg,VCF 3428_24_13_SRO_452_ATAGCGAC-mg.g.vcf.gz -V:3428_2_13_SRO_399_GTCTGTCA-mg,VCF 3428_2_13_SRO_399_GTCTGTCA-mg.g.vcf.gz -V:3428_3_13_SRO_461_GTGTTCTA-mg,VCF 3428_3_13_SRO_461_GTGTTCTA-mg.g.vcf.gz -V:3428_4_13_SRO_462_TAGGATGA-mg,VCF 3428_4_13_SRO_462_TAGGATGA-mg.g.vcf.gz -V:3428_5_13_SRO_465_TATCAGCA-mg,VCF 3428_5_13_SRO_465_TATCAGCA-mg.g.vcf.gz -V:3428_6_13_SRO_402_TCCGTCTA-mg,VCF 3428_6_13_SRO_402_TCCGTCTA-mg.g.vcf.gz -V:3428_7_13_SRO_474_TCTTCACA-mg,VCF 3428_7_13_SRO_474_TCTTCACA-mg.g.vcf.gz -V:3428_8_13_SRO_531_TGAAGAGA-mg,VCF 3428_8_13_SRO_531_TGAAGAGA-mg.g.vcf.gz -V:3428_9_14_SRO_166_TGGAACAA-mg,VCF 3428_9_14_SRO_166_TGGAACAA-mg.g.vcf.gz 
INFO  18:30:12,714 HelpFormatter - Executing as roel@utonium.nki.nl on Linux 2.6.32-504.12.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_75-b13. 
INFO  18:30:12,714 HelpFormatter - Date/Time: 2015/05/06 18:30:12 
INFO  18:30:12,715 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  18:30:12,715 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  18:30:15,963 GenomeAnalysisEngine - Strictness is SILENT 
INFO  18:30:16,109 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
INFO  18:30:29,705 IntervalUtils - Processing 101539431 bp from intervals 
WARN  18:30:29,726 IndexDictionaryUtils - Track 3428_10_14_SRO_185_TGGCTTCA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,727 IndexDictionaryUtils - Track 3428_11_14_SRO_186_TGGTGGTA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,727 IndexDictionaryUtils - Track 3428_12_13_SRO_422_TTCACGCA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,728 IndexDictionaryUtils - Track 3428_13_13_SRO_492_AACTCACC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,728 IndexDictionaryUtils - Track 3428_14_13_SRO_493_AAGAGATC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,728 IndexDictionaryUtils - Track 3428_15_14_SRO_209_AAGGACAC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,729 IndexDictionaryUtils - Track 3428_16_14_SRO_218_AATCCGTC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,729 IndexDictionaryUtils - Track 3428_17_14_SRO_201_AATGTTGC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,730 IndexDictionaryUtils - Track 3428_18_13_SRO_416_ACACGACC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,730 IndexDictionaryUtils - Track 3428_19_14_SRO_66_ACAGATTC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,730 IndexDictionaryUtils - Track 3428_1_13_SRO_388_GTCGTAGA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,731 IndexDictionaryUtils - Track 3428_20_14_SRO_68_AGATGTAC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,731 IndexDictionaryUtils - Track 3428_21_14_SRO_210_AGCACCTC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,731 IndexDictionaryUtils - Track 3428_22_14_SRO_256_AGCCATGC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,732 IndexDictionaryUtils - Track 3428_23_14_SRO_270_AGGCTAAC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,732 IndexDictionaryUtils - Track 3428_24_13_SRO_452_ATAGCGAC-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,732 IndexDictionaryUtils - Track 3428_2_13_SRO_399_GTCTGTCA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,733 IndexDictionaryUtils - Track 3428_3_13_SRO_461_GTGTTCTA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,733 IndexDictionaryUtils - Track 3428_4_13_SRO_462_TAGGATGA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,733 IndexDictionaryUtils - Track 3428_5_13_SRO_465_TATCAGCA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,734 IndexDictionaryUtils - Track 3428_6_13_SRO_402_TCCGTCTA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,734 IndexDictionaryUtils - Track 3428_7_13_SRO_474_TCTTCACA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,734 IndexDictionaryUtils - Track 3428_8_13_SRO_531_TGAAGAGA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
WARN  18:30:29,735 IndexDictionaryUtils - Track 3428_9_14_SRO_166_TGGAACAA-mg doesn't have a sequence dictionary built in, skipping dictionary validation 
INFO  18:30:29,749 MicroScheduler - Running the GATK in parallel mode with 32 total threads, 1 CPU thread(s) for each of 32 data thread(s), of 64 processors available on this machine 
INFO  18:30:29,878 GenomeAnalysisEngine - Preparing for traversal 
INFO  18:30:29,963 GenomeAnalysisEngine - Done preparing for traversal 
INFO  18:30:29,964 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  18:30:29,965 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  18:30:29,966 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  18:30:30,562 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files 
INFO  18:31:00,420 ProgressMeter -       1:4845033         0.0    30.0 s      50.3 w        0.0%    46.7 h      46.7 h 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.IllegalStateException: Key DP found in VariantContext field INFO at 1:4839315 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.
    at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:176)
    at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:115)
    at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:221)
    at org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182)
    at org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:269)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.reduce(GenotypeGVCFs.java:351)
    at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.reduce(GenotypeGVCFs.java:119)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:291)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:280)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-geee94ec):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Key DP found in VariantContext field INFO at 1:4839315 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.
##### ERROR ------------------------------------------------------------------------------------------

for f in *.g.vcf.gz; do echo -e "\n-- $f --"; zcat "$f" | sed -n -r "/^#.*DP/p;/^1\t4839315\t/{p;q;}"; done

##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839317     GT:DP:GQ:MIN_DP:PL      0/0:22:0:21:0,0,432
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839317     GT:DP:GQ:MIN_DP:PL      0/0:20:0:20:0,0,410
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839315     GT:DP:GQ:MIN_DP:PL      0/0:29:0:29:0,0,773
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839315     GT:DP:GQ:MIN_DP:PL      0/0:25:2:25:0,3,790
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839316     GT:DP:GQ:MIN_DP:PL      0/0:33:0:33:0,0,837
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839315     GT:DP:GQ:MIN_DP:PL      0/0:23:31:23:0,31,765
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       GA      G,<NON_REF>     0       .       ClippingRankSum=-0.578;MLEAC=0,0;MLEAF=0.00,0.00        GT:DP:GQ:PL:SB  0/0:21:39:0,39,488,60,491,512:20,0,0,0
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839315     GT:DP:GQ:MIN_DP:PL      0/0:18:0:18:0,0,514
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839316     GT:DP:GQ:MIN_DP:PL      0/0:29:0:29:0,0,810
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839316     GT:DP:GQ:MIN_DP:PL      0/0:33:0:33:0,0,812
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839317     GT:DP:GQ:MIN_DP:PL      0/0:28:0:25:0,0,624
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       GA      G,<NON_REF>     0.08    .       ClippingRankSum=-0.189;MLEAC=1,0;MLEAF=0.500,0.00       GT:DP:GQ:PL:SB  0/1:17:20:20,0,311,62,320,382:14,0,3,0
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       GA      G,<NON_REF>     6.76    .       ClippingRankSum=-0.374;MLEAC=1,0;MLEAF=0.500,0.00       GT:DP:GQ:PL:SB  0/1:25:43:43,0,401,102,417,519:20,0,3,2
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       GA      G,<NON_REF>     0       .       ClippingRankSum=-1.095;MLEAC=0,0;MLEAF=0.00,0.00        GT:DP:GQ:PL:SB  0/0:23:1:0,1,395,56,406,460:19,0,0,0
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839317     GT:DP:GQ:MIN_DP:PL      0/0:28:0:28:0,0,626
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       GA      G,<NON_REF>     5.99    .       ClippingRankSum=-0.584;MLEAC=1,0;MLEAF=0.500,0.00       GT:DP:GQ:PL:SB  0/1:18:42:42,0,293,84,305,388:13,1,3,1
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839317     GT:DP:GQ:MIN_DP:PL      0/0:22:0:22:0,0,558
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       GA,<NON_REF>    6.76    .       ClippingRankSum=0.850;MLEAC=1,0;MLEAF=0.500,0.00        GT:DP:GQ:PL:SB  0/1:19:43:43,0,262,87,274,361:12,3,4,0
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       GA      G,<NON_REF>     16.82   .       ClippingRankSum=-0.784;MLEAC=1,0;MLEAF=0.500,0.00       GT:DP:GQ:PL:SB  0/1:21:54:54,0,352,102,367,470:16,0,4,1
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839317     GT:DP:GQ:MIN_DP:PL      0/0:26:0:25:0,0,419
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839316     GT:DP:GQ:MIN_DP:PL      0/0:30:0:30:0,0,771
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839315     GT:DP:GQ:MIN_DP:PL      0/0:34:77:34:0,78,1136
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       G       <NON_REF>       .       .       END=4839316     GT:DP:GQ:MIN_DP:PL      0/0:26:0:20:0,0,397
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
1       4839315 .       GAA     G,GA,<NON_REF>  22.75   .       ClippingRankSum=-2.181;MLEAC=0,1,0;MLEAF=0.00,0.500,0.00        GT:DP:GQ:PL:SB  0/2:11:22:60,22,209,0,87,104,63,153,113,176:4,2,3,0

Created 2014-12-29 04:16:57 | Updated | Tags: format variant-annotation
Comments (7)

Hi,

Not sure whether this is the right place to put this, or even the right forum to ask but I was wondering whether it was possible to add custom annotations to the FORMAT field rather than the INFO field? If not GATK, do any third party programs able to handle such a request?

Thanks! Appreciate any help.


Created 2013-10-25 18:32:30 | Updated | Tags: baserecalibrator variantstovcf format
Comments (1)

I am trying to format files for input into the BaseRecalibrator and VariantsToVcf tools. Many of the links for file formats listed on the 'variant' option do not work (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToVCF.html#--variant). I get the following message: **Not Found

The requested URL /gatk/gatkdocs/org_broad_tribble_bed_BEDCodec.html was not found on this server.**

Do you know what the problem is?