GATK-Depth of Coverage - Issue with per gene coverage

Question

[ttom]

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

[Danielk]

Did you try the GATK forum? They are usually fast and give good advice. http://gatkforums.broadinstitute.org/categories/ask-the-team

[ttom]

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.

[Vivek]

Does the chromosome naming convention in Homo_sapiens_assembly19.fasta and BAM files follow the convention in the refseq file?

Answer 1

[ttom]

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