BEDtools: intersect bed on delly v0.7.8 VCF output

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2.8 years ago

Helena • 0

I'm trying to blacklist certain regions in my delly SV calls. This is the command I used:

sed -e 's/chr//g' delly_output.vcf |     bedtools intersect -v -header -a stdin -b blacklist_region.vcf >  filtered.vcf

This generated an error:

Error: Invalid record in file stdin. Record is 
2   37585630    BND00263668_2   C   <BND>   .   PASS    CE=1.89764;CIEND=-5,5;CIPOS=-5,5;CONSENSUS=ACCCCAAAAGCACAGGCAACTGAAGCAAAAATAGACAAATGGGATTGCATCAAACTAAAAAGCTTCCTTGGTTTTTTGTTTGTTTGTTTGTTTTGTTTTGTTTTGTTTTGTTGTTTAACAG;CT=3to3;HOMLEN=5;INSLEN=0;MAPQ=60;MATECHROM=12;MATEID=BND00263668_1;MATEPOS=71294327;MATESTRAND=+;PE=19;PRECISE;SOMATIC;SR=10;SRQ=1;STRAND=+;SVMETHOD=EMBL.DELLYv0.7.8;SVTYPE=BND  GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/1:-26.2549,0,-117.651:10000:PASS:125:268:142:2:66:17:38:12    0/0:0,-8.13419,-131.594:81:PASS:82:178:108:2:53:2:38:1

I suspect the issue is in the ALT column. However, I'm not sure how to work around this. Any suggestions will be much appreciated.

SV bedtools intersectbed delly VCF • 865 views

ADD COMMENT • link 2.8 years ago by Helena • 0

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sed -e 's/chr//g' delly_output.vcf

don't. Use bcftools annotate --rename-chrs

ADD REPLY • link 2.8 years ago by Pierre Lindenbaum 161k

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(...) bedtools intersect -v -header -a stdin -b blacklist_region.vcf

you want bcftools isec

ADD REPLY • link 2.8 years ago by Pierre Lindenbaum 161k

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I want to keep all the columns in the delly_output.vcf since I want to convert it into a BEDPE file downstream

ADD REPLY • link 2.8 years ago by Helena • 0

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