Dindel VCF to GATK BED or other formats

[adrian]

Hi:

I have final output files (after stage4) in VCF format from Dindel.

I want to annotate the indel calls using SeattleSeq annotation pipeline. This tool needs either BED file or GATK BED file (for indels) or other formats including VCF.

The VCF file that Dindel outputs, when given as input to SeattleSeq, I get the file has several errors and cannot run.


How can I convert Dindel VCF file to GATK bed file or regular BED file.

Also are there any other annotation pipelines to anntoate indel and snp calls in addition to SeattleSeq.

Thanks!