Dear samtools community, I have a 10bp deletion called with DP=42 and DP4=0,6,0,16 and IDV=8. There is no second variant allele called at this site.
Looking at the alignment manually, I see exactly 8 reads showing the deletion. This is consistent with IDV=8. And I see a total of 42 reads (including the 8 deletion reads) spanning the position, which is consistent with DP=42. I have checked both base- and mapping qualities (e.g. samtools depth -q 15 -Q 15 also gives 42) and they seem not responsible for the DP4 calls. And I cannot understand how the third and fourth position of DP4 (0,16) can be larger than IDV (8). I hope someone can explain this to me. And if 42 reads/bases are of high quality, how can the sum over DP4 be so small (22)? I am using samtools 1.3.1 and bcftools 1.3.1 (but have seen the same issue with samtools 0.1.18 as well). The commandlines were samtools mpileup -u -q 15 -f hg19.fa -m 3 -F 0.03 -B -d 10000000 -L 10000000 -l <(echo -e "chr1\t237955648\t237955649") case.bam | bcftools call -c - This is the VCF result (excluding headers): chr1 237955649 . C . 155.995 . DP=42;MQSB=1;MQ0F=0;AF1=0;AC1=0;DP4=3,39,0,0;MQ=60;FQ=-152.987GT:PL 0/0:0 chr1 237955649 . CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGT CTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGT 217.469 . INDEL;IDV=8;IMF=0.190476;DP=42;VDB=7.68124e-06;SGB=-0.689466;MQ0F=0;AF1=0.50002;AC1=1;DP4=0,6,0,16;MQ=60;FQ=7.35744;PV4=1,1,1,0.276636 GT:PL 0/1:255,0,41 Best regards, Florian Battke -- Dr. Florian Battke Associate Director Bioinformatics & IT Fon. +49 (0)7071 565 44 55 Fax. +49 (0)7071 565 44 56 ------------------------------------------------------ CeGaT GmbH | Paul-Ehrlich-Str. 23 | 72076 Tuebingen, Germany [email protected] | www.cegat.de Court District Stuttgart - HRB 729958 | VAT-No.: DE265504070 Managing Directors: Dr. Dr. Saskia Biskup, Dr. Dirk Biskup ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
