Tagged with #i
0 documentation articles | 0 announcements | 2 forum discussions

No posts found with the requested search criteria.
No posts found with the requested search criteria.

Created 2015-09-11 15:35:09 | Updated 2015-09-11 15:35:29 | Tags: intervals mutect b37 i reference-error
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




Thanks a ton for your help!

Created 2013-12-09 13:00:14 | Updated | Tags: developer intervals walker i
Comments (4)


Recently I've been wanting to preform tasks for each interval in a file using the GATK. Are you guys planning to create an IntervalWalker class? (Or is there a workaround?) DiagnoseTargets in gatk-protected seem to work this way, but not in a very straightforward way - also since it's protected I'm not sure how much if any code I could borrow from there.

cheers Daniel