Hello,
I am working with the output from a bcftools -cgA command, and it seems to be different from the VCF specification.
In particular it seems to show in some positions in the gene a REF as a string of various letters and in the ALT only a dot (see screenshot). The INFO field calls an INDEL. I assume that this means a deletion, and that the ALT is only the first base, in the following manner:
REF= CGGGT #sequence should be ...CGGGT...
ALT= . #sequence is ...C...
However, the VCF 4.1 format would call for a C instead of a dot (see screenshot). The header of the file specifies:
##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
I'm I correct in my interpretation of the deletion?
Thank you,
Keo.
I am working with the output from a bcftools -cgA command, and it seems to be different from the VCF specification.
In particular it seems to show in some positions in the gene a REF as a string of various letters and in the ALT only a dot (see screenshot). The INFO field calls an INDEL. I assume that this means a deletion, and that the ALT is only the first base, in the following manner:
REF= CGGGT #sequence should be ...CGGGT...
ALT= . #sequence is ...C...
However, the VCF 4.1 format would call for a C instead of a dot (see screenshot). The header of the file specifies:
##fileformat=VCFv4.1
##samtoolsVersion=0.1.18 (r982:295)
I'm I correct in my interpretation of the deletion?
Thank you,
Keo.
Comment