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Why was this call filtered out?

General Discussion
Erik Reckase
2016-03-28
2016-03-29

  • Erik Reckase

    Erik Reckase - 2016-03-28

    Can someone tell me why a call was not made at this location?

    lofreq call -f /var/www/hg19.fa --min-bq 0 --min-alt-bq 0 --bed foo.bed --verbose --debug -a 0.1 -b 1 --min-mq 0 foo.bam

    DEBUG(plp.c|compile_plp_col): Processing chr3:178936091
chr3    178936091   G   G   counts:rv/fw A:8/10 C:1/0 G:216/627 T:0/4 N:0/0 heads:0 tails:3 ins:0 del:0 hrun=1
DEBUG(lofreq_call.c|call_snvs): chr3 178936091: passing down 866 quals with noncons_counts (18, 1, 4) to snpcaller(num_snv_tests=15 conf->bonf=1, conf->sig=0.100000)
     

    • Andreas Wilm

      Andreas Wilm - 2016-03-29

      Hi Erik,

      hard to tell from this output. Might be because of strand bias. Could
      you rerun with '-r chr3:178936091-178936091 --no-default-filter' and
      see what the variant and SB qualities are?

      Thanks,
      Andreas

      On 29 March 2016 at 01:13, Erik Reckase ereckase@users.sf.net wrote:

      Can someone tell me why a call was not made at this location?

      lofreq call -f /var/www/hg19.fa --min-bq 0 --min-alt-bq 0 --bed foo.bed
      --verbose --debug -a 0.1 -b 1 --min-mq 0 foo.bam

      DEBUG(plp.c|compile_plp_col): Processing chr3:178936091
      chr3 178936091 G G counts:rv/fw A:8/10 C:1/0 G:216/627 T:0/4 N:0/0
      heads:0 tails:3 ins:0 del:0 hrun=1
      DEBUG(lofreq_call.c|call_snvs): chr3 178936091: passing down 866 quals with
      noncons_counts (18, 1, 4) to snpcaller(num_snv_tests=15 conf->bonf=1,
      conf->sig=0.100000)

      Why was this call filtered out?

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      --
      Andreas Wilm
      andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC

       

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