not giving unique values when doing intersectBed between VCF file and BED file

23 views
Skip to first unread message

AA D

unread,
Mar 3, 2023, 9:30:13 AM3/3/23
to bedtools-discuss
hey I am facing this issue any idea why?So my vcf contains these :
chr1 201784568 . T A . . DP=12;MQ=60.00;TLOD=5.06;FractionInformativeReads=1.000 GT:SQ:AD:AF:> chr1 201785282 . CTTTTT C . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=4.43;Fract> chr1 201785282 . CTTTTT CT . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=9.28;Fract> chr1 201785282 . CTTTTT CTT . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=4.38;Fract> chr1 201785282 . CTTTTT CTTT . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=13.77;Frac>
when i intersect  it with the bed file i had obtained after sorting from the below cmd:
sort -t $'\t' -k1,1 -k2,2n k75.bed | bgzip > k75_sorted.bed.gzThe intersect cmd is:
cat <(grep "#" Horizon_44799.HD827.hg38.raw.other_variants.dragen.vcf) <(/usr/local/mrgstorage/software/BEDTools/bin/intersectBed -a Horizon_44799.HD827.hg38.raw.other_variants.dragen.vcf -b k75_sorted.bed.gz -u ) > test.vcfwhy am i not getting the unique values in test.vcf though I use -u
chr1 201785282 . CTTTTT C . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=4.43;Fract> chr1 201785282 . CTTTTT CT . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=9.28;Fract> chr1 201785282 . CTTTTT CTT . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=4.38;Fract> chr1 201785282 . CTTTTT CTTT . . DP=123;MQ=60.00;MQRankSum=8.531;ReadPosRankSum=0.518;TLOD=13.77;Frac> chr1 201785316 . G C . . DP=152;MQ=60.00;TLOD=32.59;FractionInformativeReads=1.000 GT:S> chr10 43100520 . A G . . DP=236;MQ=60.00;TLOD=255.77;FractionInformativeReads=0.996 GT:S> chr10 43105241 . A G . . DP=294;MQ=60.00;TLOD=104.69;FractionInformativeReads=0.997 GT:S> chr10 43109045 . C T . . DP=265;MQ=60.00;TLOD=280.07;FractionInformativeReads=0.992 GT
Reply all
Reply to author
Forward
0 new messages