I have a vcf file (sample1.vcf)< and I will like to remove a large list of sites contained in a bedfile
e.g.:
chr22 37536301 37536301
chr22 82722119 82722273
chr18 218879484 218879484
chr18 60949121 60949149
chr13 230905465 230905465
The command I run:
intersectBed -a sample1.vcf -b hg19.sorted.bed -v
results in
intersectBed: line 2: 21108 Segmentation fault (core dumped) ${0%/*}/bedtools intersect "$@"
How can I fix this?
If the segmentation fault is due to excessive memory requirements, sort your bed files by chromosome and position (with sort -k1,1 -k2,2n a.bed > sorted.bed) and then use the -sorted option of intersectBed :
If you are trying to intersect very large files and are having trouble with excessive memory usage, please presort your data by chromosome and then by start position (e.g.,
sort -k1,1 -k2,2n in.bed > in.sorted.bedfor BED files) and then use the-sortedoption. This invokes a memory-efficient algorithm designed for large files. This algorithm has been substantially improved in recent (>=2.18.0) releases.
Also, a quick check to see if your files are already sorted is to use the -c option in sort:
sort -c -k1,1 -k2,2n a.bed
For what it's worth, I just got around a bedtools intersect segmentation fault by upgrading bedtools
One alternative, using bash redirection:
bedops --not-element-of -1 <(convert2bed -i vcf < sample1.vcf) hg19.sorted.bed > answer.bed
The convert2bed tool applies sort-bed ordering on the converted VCF.
If you don't know the sort status of hg19.sorted.bed (in spite of its name), then you can do similar redirection with that second input to make sure it is sorted:
bedops --not-element-of -1 <(convert2bed -i vcf < sample1.vcf) <(sort-bed hg19.sorted.bed) > answer.bed
The sort-bed application is usually faster than GNU sort at sorting BED files for use with BEDOPS or other tools, but either will work.
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Alex Reynolds
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I hope you read through the rest of the segmentation fault posts on the site. There are issues with unsorted and unindexed files that are explained in many different posts.
yes I have, non of the suggested solutions work
In the meantime, try
vcftools --exclude-positions <bedfile>from here: http://vcftools.sourceforge.net/man_latest.htmlthanks, working solution