Entering edit mode
4.9 years ago
duolin1
▴
10
when I using snpsift software filter vcf by coordinate of bed, I found the result of vcf have wrong item that non_exist in bed ;
this is bed's coordinate
chr8 29608637 29609316
chr8 29609651 29609846
this is the "wrong" item that I found in result that is filtered by bed
< chr7 123666723 . AT A 207.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.749;ClippingRankSum=0.860;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.39;MQ0=0;MQRankSum=-0.416;QD=7.42;ReadPosRankSum=-0.250;SOR=0.495 GT:AD:DP:GQ:PL 0/1:13,15:28:99:245,0,194
< chr8 29609647 . TAAAAAGA T 179.73 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.167;ClippingRankSum=-1.303;DP=23;FS=2.066;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.702;QD=7.81;ReadPosRankSum=0.634;SOR=1.402 GT:AD:DP:GQ:PL 0/1:16,7:23:99:217,0,976
as you can see ,actually this is "wrong" item because this "chr8...." is not accord with bed's coordinate; by the way, I found the wrong item often happened in the first item of the new "chr"( it can also see in my provided item)
this is my code like this
cat variants.vcf | java -jar SnpSift.jar intervals my_intervals.bed > variants_intersecting_intervals.vcf
so,my question is why , is it a bug in snpsift???
which version of snpsift ?
how about just using
bcftools view
?I'd report it to the SnpSift author.
It is a 7bp deletion which overlaps your specified coordinate so it might make sense depending on how you look at it. I would prefer to have such hits in my results.
thank you very much. I understand..