Hi all,
I have produced a vcf file of aligned sequence data using samtools mpileup, with the -D flag set.
For some reason certain lines lack the "DP4=" information, eg:
1 124157647 . G . 33 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=60;FQ=-30 PLP 0:1
1 124157648 . T . 28.2 . DP=1;;AC1=2;FQ=-30 PLP 0:0
I have a bespoke SNP calling program that relies on this information to make calls. I have not encountered this problem before. Any suggestions on how to correct this?
Thanks in advance
I have produced a vcf file of aligned sequence data using samtools mpileup, with the -D flag set.
For some reason certain lines lack the "DP4=" information, eg:
1 124157647 . G . 33 . DP=1;AF1=0;AC1=0;DP4=1,0,0,0;MQ=60;FQ=-30 PLP 0:1
1 124157648 . T . 28.2 . DP=1;;AC1=2;FQ=-30 PLP 0:0
I have a bespoke SNP calling program that relies on this information to make calls. I have not encountered this problem before. Any suggestions on how to correct this?
Thanks in advance