vcf2bed

[sco...@gmail.com]

Hi all,

I used vcf2bed to transform methylation and SNP calls and the bed file I get has much less rows than the calls in the vcf file. All the rows in my vcf is PASS. With a similar utility from bedops I get different results. Do you know why this might happen?

Thanks in advance,

Anna

[ping]

Hi Anna,

Vcf2bed.pl is used to transform methylation vcf to bed format. When CG position is confidently called by its non-bisulfite converted strand, it may not have reads in bisulfite converted strand to calculate methylation level. So this will be omitted in the final bed file.

Yaping

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Yaping Liu, Ph.D.

Postdoctoral Associate

Manolis Kellis Lab

Computer Science and Artificial Intelligence Lab (CSAIL)
Massachusetts Institute of Technology

Broad Institute of MIT and Harvard

Office Phone: +1 617 324 8436 
Email: 

lypin...@gmail.com

yap...@mit.edu

lyp...@broadinstitute.org