Convert Indel format in vcf

Question

[mavershang]

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

Answer 1

[Nicola Casiraghi]

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.

Answer 2

[Danielk]

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.

[mavershang]

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