Question: VCF-BEDintersect via galaxy not working for me, what am I missing?
0
gravatar for a.v.postma
11 months ago by
a.v.postma0
European Union
a.v.postma0 wrote:

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?

software error galaxy • 253 views
ADD COMMENTlink written 11 months ago by a.v.postma0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 107 users visited in the last hour