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Created 2015-09-11 15:35:09 | Updated 2015-09-11 15:35:29 | Tags: intervals mutect b37
Comments (15)

I hate to put this same error on the GATK forum again, but I went through many of these errors already posted on the forum, but none of the answers shed light on my issue. I have my bam files aligned to GRCh37-lite and am using the same reference genome downloaded from ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests

I have next performed GATK best practices for pre-processing of these bams using the same ref genome without throwing any error in the process. Currently I'm running MuTect as java -Xmx56g -jar muTect-1.1.4.jar --analysis_type MuTect --reference_sequence ./resources/b37/human_g1k_v37.fasta --cosmic ./resources/Cosmic.b37.vcf --dbsnp ./resources/dbsnp_138.b37.vcf --intervals ./resources/mirna.1.5flank-interval-list.list --input_file:normal $normal.recal_reads.bam --input_file:tumor $tumor.recal_reads.bam --out $sample.call_stats.out --coverage_file $sample.coverage.wig.txt

And getting this error message:

ERROR MESSAGE: Badly formed genome loc: Contig 'chr1' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?

What more tests should I run to troubleshoot this issue? Also, the interval list is what I created from a .bed file. I have restricted my bam files to a limited bed regions using the same file in a command "samtools view -@8 -b -h -L"

This was the file I was most confused about. Is it possible that this file is causing the error? First few lines of this file are: chr1:15869-18936 chr1:28866-32003 chr1:566205-569293 chr1:1100984-1104078 chr1:1101743-1104832 chr1:1102885-1105967 chr1:1229990-1233050 chr1:1246382-1249446 chr1:1273530-1276588 chr1:3043039-3046099 chr1:3475759-3478854 chr1:5622631-5625703 chr1:5921232-5924301 chr1:6488394-6491456 chr1:8925061-8928149 chr1:9210227-9213336 chr1:10025939-10029016 chr1:10286276-10289361 chr1:12087715-12090779



Thanks a ton for your help!

Created 2012-08-28 20:22:44 | Updated 2013-01-07 20:00:01 | Tags: hg19 b37
Comments (4)

Hi, We have some annotation files, for example a GTF file of UCSC's "Known Genes" in hg19 coordinates. We'd like to convert this to b37 coordinates. What's the best way to go about doing this? Assistance would be appreciated! Thanks in advance, Lao