The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at http://bit.ly/2i4mGxz

SelectVariants for an array

TgongTgong Member Posts: 2
edited April 2013 in Ask the GATK team

My indel calling VCF has the following information:

##INFO=<ID=N_MQ,Number=2,Type=Float,Description="In NORMAL: average mapping quality of consensus indel-supporting reads/reference-supporting reads">

so one example of my indels is:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  exom_aladaz
chr1    54690639        .       G       GCCC    .       .       N_AC=0,0;N_DP=19;N_MM=0.0,0.36842105;N_MQ=0.0,33.894737;N_NQSBQ=0.0,31.80368;N_NQSMM=0.0,0.0;N_SC=0,0,19,0;SOMATIC;T_AC=6,6;T_DP=11;T_MM=0.5,0.2;T_MQ=44.5,29.0;T_NQSBQ=30.85,33.36;T_NQSMM=0.016666668,0.0;T_SC=6,0,5,0  GT:GQ   0/1:0

If I want to filter indel calls with N_MQ <30 for both consensus indel-supporting reads/reference-supporting reads, how should I write the SelectVariants for N_MQ=0.0,33.894737?

Post edited by Geraldine_VdAuwera on
Tagged:

Answers

Sign In or Register to comment.