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A snip and deletion without DP in g.vcf file
I have noticed that some times g.vcf files will have calls where the DP field is completely missing from the FORMAT string, even though a variant is called with good GQ. When this happens, the INFO string does have a DP=0, as can be seen below.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 102637-001-093 gi|194447306|ref|NC_011083.1| 415537 . A <NON_REF> . . END=415547 GT:DP:GQ:MIN_DP:PL 0:2:86:2:0,86 gi|194447306|ref|NC_011083.1| 415548 . G A,<NON_REF> 13.22 . DP=0;MLEAC=1,0;MLEAF=1.00,0.00;RAW_MQ=0.00 GT:GQ:PL:SB 1:43:43,0,43:0,0,0,0 gi|194447306|ref|NC_011083.1| 415549 . A <NON_REF> . . END=415549 GT:DP:GQ:MIN_DP:PL 0:2:86:2:0,86 gi|194447306|ref|NC_011083.1| 4683672 . A <NON_REF> . . END=4683672 GT:DP:GQ:MIN_DP:PL 0:2:0:2:0,0 gi|194447306|ref|NC_011083.1| 4683673 . AATC A,<NON_REF> 6.95 . DP=0;MLEAC=1,0;MLEAF=1.00,0.00;RAW_MQ=0.00 GT:GQ:PL:SB 1:45:45,0,45:0,0,0,0 gi|194447306|ref|NC_011083.1| 4683677 . A <NON_REF> . . END=4683677 GT:DP:GQ:MIN_DP:PL 0:1:0:1:0,0
I'm using gatk version 3.5-0-g36282e4, and I've attached the files I used. The exact command I used is as folows:
bamfile=093_interval.bam output=093_interval.g.vcf bamout=093_interval_bamout.bam reference=NC_011083.fasta gatk -T HaplotypeCaller \ --sample_ploidy 1 \ -R $reference \ -I $bamfile \ -o $output \ -ERC GVCF \ -bamout $bamout
How can I make sense of this, to my mind DP=0 (from the INFO field at least) should mean there are no reads, so therefore no call can be made, right?