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twolinin / longphase

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empty output #22

Open ChannieJ opened 2 years ago

ChannieJ commented 2 years ago

filter mapping quality below: 20 percentage threshold: 0.6 tag supplementary: false

parsing SNP VCF ... 26s tag read start ... tag read 0s

total process time: 26s total alignment: 0 total supplementary: 0 total secondary: 0 total unmapped: 0 total tag alignment: 0 total untagged: 0

I don't know how to solve this problem?

twolinin commented 2 years ago

Hi @ChannieJ , Please help me check

  1. Whether the phased vcf file has reference information, i.e. 
    ##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
.
.
  2. Whether the phased vcf file has phased SNPs. You can check if the PS in the vcf field has a value, i.e. 
    1       13896   .       C       A       4.1     PASS    .       GT:GQ:DP:AD:VAF:C:PS    1|0:4:14:5:0.357143:DV:13896
1       15118   .       A       G       10.1    PASS    .       GT:GQ:DP:AD:VAF:C:PS    0|1:6:14:9:0.642857:DV:13896
1       15820   .       G       T       5.4     PASS    .       GT:GQ:DP:AD:VAF:C:PS    1|0:5:15:7:0.466667:DV:13896

thanks