johjoon

mosdepth in multiple region

1

hello, I came across a trouble. I have to calculate the depth in all autosomes, in other words, I have to exclude the MT area. I want to know whether...

bcftools norm --multialllelics -both v1.8 does not split FORMAT/AS_FilterStatus correctly

4

hello， In my vcf after splitting multiallelic sites, the info was separated wrongly, like this Before splitting ``` chrM 16189 . T C,A . PASS AS_FilterStatus=SITE|weak_evidence,base_qual,strand_bias,possible_numt; GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:3,2016,22:0.995,4.028e-03:2041:1,814,6:2,1101,3:0,3,659,1379 ``` After...

some problems in using bcftools norm command

1

I found that some duplicated variants appeared while normalize some big indel while using bcftools norm It failed to combine the two variants as below variant1： chr: bp: TTCACTCATTCATCACTAACCCATTGACTCACTCACTCAATCACTCATTCACTCACTCAATCACTCATTCACTCATTAACCCATTGACTCACTCCCTCAATCACTCATTCACTCACTAACCCATTGACTCACTCACTCATTCACTCACTAACCCATTGACTCACTCAATCACTCATTCATTCACTAACCCATTGACTCACTCACTCGATCACTCATTCACTCACTCATTCACTCATTCACTAACCCATTCAGTCACTCAA:T AC=5;DP=5...