Paul Wang - 2014-01-09

Hi again,

I think the header is also missing lines about 'naf' and 'daf'.

On Thu, Jan 9, 2014 at 3:11 PM, Paul Wang ppswang@gmail.com wrote:

Hi,

I am using Virmid v 1.1.0.

I believe there is an error in the VCF output header.

In the INFO lines:

INFO=<ID:NDP,Number=1,Type=Integer,Description="Read depth in control

sample">

INFO=<ID:NAC,Number=1,Type=Integer,Description="Allele count in control

sample">

INFO=<ID:DDP,Number=1,Type=Integer,Description="Read depth in disease

sample">

INFO=<ID:DAC,Number=1,Type=Integer,Description="Allele count in disease

sample">

INFO=<ID:mq,Number=1,Type=Float,Description="Mean mapping quality of

reference reads">

INFO=<ID:mqmis,Number=1,Type=Float,Description="Mean mapping quality of

mismatch containing reads">

INFO=<ID:mq30,Number=1,Type=Float,Description="Ratio of reads whose

mapping quality is less than 30">

INFO=<ID:off,Number=1,Type=Integer,Description="Expected position of

alternative allele in the read (read length/4)">

INFO=<ID:offmis,Number=1,Type=Float,Description="Mean end-position of

alternative allele in the read">

INFO=<ID:prx,Number=1,Type=Float,Description="Ratio of reads that are

closely located nearby indels">

INFO=<ID:prxmis,Number=1,Type=Float,Description="Ratio of alternative

alleles that are closely located nearby indels">

INFO=<ID:majorAF,Number=1,Type=Float,Description="Major allele

frequency">

INFO=<ID:bqmis,Number=1,Type=Float,Description="Mean base call quality

of alternative alleles">

INFO=<ID:nm,Number=1,Type=Float,Description="Mean number of mismatches

per read">

INFO=<ID:clip,Number=1,Type=Float,Description="Ratio of soft (hard)

clipped read">

They should be "ID=", not "ID:"