Question: BedTools IntersectBed resulting in Segmentation Fault with BedFile
gravatar for ali
4.3 years ago by
ali0 wrote:

I have a vcf file (sample1.vcf)< and I will like to remove a large list of sites contained in a bedfile


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?


intersectbed vcf bedfile bedtools • 5.5k views
ADD COMMENTlink modified 4.3 years ago by dariober9.9k • written 4.3 years ago by ali0

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.

ADD REPLYlink written 4.3 years ago by RamRS20k

yes I have, non of the suggested solutions work

ADD REPLYlink written 4.3 years ago by ali0

In the meantime, try vcftools --exclude-positions <bedfile> from here:

ADD REPLYlink written 4.3 years ago by RamRS20k

thanks, working solution

ADD REPLYlink written 4.3 years ago by ali0
gravatar for dariober
4.3 years ago by
WCIP | Glasgow | UK
dariober9.9k wrote:

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.bed for BED files) and then use the -sorted option. 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

ADD COMMENTlink written 4.3 years ago by dariober9.9k
gravatar for Alex Reynolds
4.3 years ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

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.

ADD COMMENTlink modified 4.2 years ago • written 4.3 years ago by Alex Reynolds27k
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