Hi,
Im trying to select certain lines in a vcf file that fall within certain genomic regions (BED file). For this I used the VCF-BEDintersect via galaxy (After uploading a bonafide vcf and bed file) I dont get any results after intersection. The tool works, there are just no resulting vcf lines (only comment lines). I feel like Im missing something fundamental.
vcf example of 3 lines
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
1 877831 rs6672356;COSM4144217 T C 959.77 PASS AAChange.refGene=SAMD11:NM_152486:exon10:c.T1027C:p.W343R;ANNOVAR_DATE=2016-02-01;ExonicFunc.refGene=nonsynonymous_SNV;Func.refGene=exonic;Gene.refGene=SAMD11;GeneDetail.refGene=. GT:AD:DP:GQ:PL 1/1:0,34:34:99:988,101,0 1/1:0,16:16:48:478,48,0 1 881627 rs2272757;COSM1344685 G A 341.77 PASS AAChange.refGene=NOC2L:NM_015658:exon16:c.C1843T:p.L615L;ANNOVAR_DATE=2016-02-01;ExonicFunc.refGene=synonymous_SNV;Func.refGene=exonic;Gene.refGene=NOC2L;GeneDetail.refGene=. GT:AD:DP:GQ:PL 0/1:20,16:36:99:370,0,568 1/1:0,32:32:96:1045,96,0 1 887801 rs3828047;COSM426785 A G 1301.77 PASS AAChange.refGene=NOC2L:NM_015658:exon10:c.T1182C:p.T394T;ANNOVAR_DATE=2016-02-01;ExonicFunc.refGene=synonymous_SNV;Func.refGene=exonic;Gene.refGene=NOC2L;GeneDetail.refGene=. GT:AD:DP:GQ:PL 1/1:0,40:40:99:1330,120,0 1/1:0,19:19:57:638,57,0
bed region that encompass the variants from the above three lines chr1 877821 877841 chr1 881620 8876901
the result return only comment lines, no vcf variant lines. What am I doing wrong?