Hello All
I ran Dindel to search for indels and was successfully ended up with a VCF output file. When I checked the validity of the VCF file with vcftools it came up with a lot of errors such as:
column SAMPLE at 1:215054083 .. Bad ALT value in the GT field, the index [2] out of bounds [1/2].
The following is the indel call from the VCF file:
1 215054083 . G GA 215 PASS DP=119;NF=19;NR=12;NRS=27;NFS=25;HP=3 GT:GQ 1/2:164
There is no second allele specified on ALT even though the GT field refers to it.
I was wondering if anyone else has ended up with these inconsistencies after using Dindel? And how did you end up fixing it?
Thanks
Dave
I ran Dindel to search for indels and was successfully ended up with a VCF output file. When I checked the validity of the VCF file with vcftools it came up with a lot of errors such as:
column SAMPLE at 1:215054083 .. Bad ALT value in the GT field, the index [2] out of bounds [1/2].
The following is the indel call from the VCF file:
1 215054083 . G GA 215 PASS DP=119;NF=19;NR=12;NRS=27;NFS=25;HP=3 GT:GQ 1/2:164
There is no second allele specified on ALT even though the GT field refers to it.
I was wondering if anyone else has ended up with these inconsistencies after using Dindel? And how did you end up fixing it?
Thanks
Dave