GATK-Depth of Coverage - Issue with per gene coverage
1
0
Entering edit mode
10.2 years ago
ttom ▴ 220

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
GATK DepthOfCoverage • 8.1k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
10.2 years ago
ttom ▴ 220

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
ADD COMMENT

Login before adding your answer.

Traffic: 5264 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6