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Convert Indel format in vcf

Hi there,

Say I have a insertion (on GRCh37) in format

1    866511    rsXXXXXX    -    CCCT  INFO_Field_BLABLA

Is there any existing tools I can use to include the previous ref nucleotide and convert it to

1    866510    rsXXXXXX    A   ACCCT  INFO_Field_BLABLA

Thanks in advance

indel snp
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updated by Ram Ram • written by mavershang mavershang

2 answers

Hi, you can retrieve the reference allele at a specific position using samtools faidx (or bedtools getfasta) and then, playing with a little bit of scripting, you should arrange this information to get your desired output format.

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updated by Ram Ram • written by Nicola Casiraghi Nicola Casiraghi

Bcftools will do that for you. Check out the command bcftools norm.

Edit: It's possible that vt normalize or GATK LeftAlignAndTrimVariants might also work for this.

• 1 views • link
updated by Ram Ram • written by Danielk Danielk

The program failed with error "core dump". So finally I wrote my own code to solve the problem. Thanks

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written by mavershang mavershang

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