I am trying to use GATK DepthOfCoverage to get coverage across a list of genes along with an interval file. I tried this with GATK-3.0 and also in GATK-3.1
I am getting only one output which looks like depth for all positions in the interval file for all samples. I am not getting any additional file for per gene coverage.
java -Xmx8g -jar GenomeAnalysisTK.jar -R Homo_sapiens_assembly19.fasta -T DepthOfCoverage \
--calculateCoverageOverGenes:REFSEQ Genes_refgene.txt \
--outputFormat table -o Coverage_summary -I BAM.list -L genes.bed
head Genes_refgene.txt
791 NM_139135 1 + 27022521 27108601 27022894 27107247 20 "27022521,27056141,27057642,27059166,27087346,27087874,27088642,27089463,27092711,27092947,27094280,27097609,27098990,27099302,27099836,27100070,27100292,27101470,27102067,27105513," "27024031,27056354,27058095,27059283,27087587,27087964,27088810,27089776,27092857,27093057,27094490,27097817,27099123,27099478,27099987,27100208,27100389,27101711,27102198,27108601," 0 ARID1A cmpl cmpl "0,0,0,0,0,1,1,1,2,1,0,0,1,2,1,2,2,0,1,0,"
791 NM_006015 1 + 27022521 27108601 27022894 27107247 20 "27022521,27056141,27057642,27059166,27087346,27087874,27088642,27089463,27092711,27092947,27094280,27097609,27098990,27099302,27099836,27100070,27100292,27100819,27102067,27105513," "27024031,27056354,27058095,27059283,27087587,27087964,27088810,27089776,27092857,27093057,27094490,27097817,27099123,27099478,27099987,27100208,27100389,27101711,27102198,27108601," 0 ARID1A cmpl cmpl "0,0,0,0,0,1,1,1,2,1,0,0,1,2,1,2,2,0,1,0,"
1464 NM_002524 1 - 115247084 115259515 115251155 115258781 7 "115247084,115250774,115251151,115252189,115256420,115258670,115259278," "115250671,115250813,115251275,115252349,115256599,115258798,115259515," 0 NRAS cmpl cmpl "-1,-1,0,2,0,0,-1,"
head genes.bed
1 27022533 27022634 ARID1A
1 27022883 27022964 ARID1A
1 27023112 27023498 ARID1A
1 27023499 27023788 ARID1A
1 27056114 27056354 ARID1A
1 27057616 27058125 ARID1A
1 answer
The chromosome naming convention in the reference fasta file, BAM files, RefSeq file and interval file were same.
I could troubleshoot this issue, So the problem was with RefSeq file, in the sorting. It was sorted according to chromosome, but not according to positions. I kept getting per sample coverage file and not any other output from DepthOfCoverage
sorting command used
sort -nk3 -nk5 Genes_refgene.txt > Genes_refgene.sorted.txt
Ran DepthOfCoverage
Got the following output files
Coverage_summary
Coverage_summary.sample_cumulative_coverage_counts
Coverage_summary.sample_cumulative_coverage_proportions
Coverage_summary..sample_gene_summary
Coverage_summary..sample_interval_statistics
Coverage_summary.sample_interval_summary
Coverage_summary..sample_statistics
Coverage_summary..sample_summary
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Did you try the GATK forum? They are usually fast and give good advice. http://gatkforums.broadinstitute.org/categories/ask-the-team
Yes I did try.
Here is the same question I posted there. http://gatkforums.broadinstitute.org/discussion/4075/depth-of-coverage-only-one-type-of-output#latest
Didnot get to solve this there, so posted here.
Does the chromosome naming convention in
Homo_sapiens_assembly19.fastaand BAM files follow the convention in the refseq file?