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Weird observation in FORMAT column DP from Unified Genotyper

newbie16newbie16 Member Posts: 42
edited January 2013 in Ask the GATK team


I am trying Unified Genotyper on a 454 data set combined with some artificial data. The bam file for this data has 12 aligned reads spanning the locus: Chr17:7578406. These 12 reads are obtained from real 454 run.
On executing Unified Genotyper with the following options:

java -Xmx4g -jar /usr/local/lib/GenomeAnalysisTK-2.2-15-g9214b2f/GenomeAnalysisTK.jar -R ~/CGP/ReferenceSeq/fromGATK/bundle1.5/b37/human_g1k_v37.fasta -T UnifiedGenotyper -I NG.CL316.ordered.sorted.bam -o NG.1x.CL316.vcf --dbsnp ~/CGP/ReferenceSeq/fromGATK/bundle1.5/b37/dbsnp_135.b37.vcf -stand_call_conf 30 -stand_emit_conf 0.0 -dcov 5000 -L "17:7,578,400-7,578,410"

I get the following result:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  z
17      7578406 rs28934578      C       T       83.77   .       AC=1;AF=0.500;AN=2;BaseQRankSum=-0.529;DB;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=2.7884;MLEAC=1;MLEAF=0.500;MQ=38.06;MQ0=0;MQRankSum=0.529;QD=6.98;ReadPosRankSum=2.367     GT:AD:DP:GQ:PL  0/1:7,5:12:99:112,0,195

Then I added a copy of same 12 reads (after modifying the names of the added reads to give each added read a unique name) to the above bam file. I have ensured that the names are unique in the bam file. Then again I run UnifiedGenotyper and get the following result:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  z
17      7578406 rs28934578      C       T       165.77  .       AC=1;AF=0.500;AN=2;BaseQRankSum=-0.966;DB;DP=24;Dels=0.00;FS=1.885;HaplotypeScore=5.5768;MLEAC=1;MLEAF=0.500;MQ=38.06;MQ0=0;MQRankSum=0.205;QD=6.91;ReadPosRankSum=3.367     GT:AD:DP:GQ:PL  0/1:14,10:22:99:194,0,363

I want to point out that in the first run, I see that INFO and FORMAT column's have DP=12 and AD of 7,5 add up indicating that no read for filtered for making the variant call. However in the second run, even though the 12 extra reads are exactly the same as the earlier 12 reads, we see that while the INFO column DP=24, the FORMAT column DP is 22. Which indicates that 2 reads have been filtered while making the variant call.

Also please note that I tried adding the 12 read incrementally. And observed that till adding the 7th read, the DPs were all matching up. But then when I added the 8th read, the result showed that 2 reads were filtered (from FORMAT column DP). So if only the 8th read was being filtered out, I would think it might be a problem with that read but why is an extra read which was not being filtered earlier is being filtered on addition of this read. Or is the FORMAT column DP incorrect?

The 12 aligned reads that were added to the sam file are attached. Please let me know if you would need any other info.

Thanks for any insight in this issue.

Post edited by Geraldine_VdAuwera on

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 10,738 admin

    Have you tried changing the order in which you add the extra reads? Is it always the same added read that causes the problem?

    Geraldine Van der Auwera, PhD

  • newbie16newbie16 Member Posts: 42


    So I did try changing the order in which I added the reads and it seems that a particular read is NOT the problem. But it seems that when I incrementally add the reads, adding the 8th read (irrespective of what the read is) is when I start getting the weird DP count (2 less than it is supposed to be).
    I tried this 2 ways.
    First I added the reads in reverse order as before. When I added the 8th read, the FORMAT column DP was 18 (It should be 20 if no reads were filtered)
    Then I used one read and created 12 identical reads except that I changed their names. Again when I added them incrementally, it was the addition of 8th read that started the weird DP.


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