How to extract both start and end position in vcf files

Question

[ShirleyDai]

Hello, I have some vcf files generated from GATK mutect2. I can use GATK VariantsToTable to extract start position of each variants. I wonder if there is an easy way to extract both start and end position in my vcf files. Thanks

Answer 1

[venu]

You mean start and end position of variants? If yes, following will work

(Updated)

vcf-annotate --fill-type Sample1.vcf | grep '^chr' | awk '{if($8 ~ /snp/)print $1"\t"$2"\t"$2"\t"$4"\t"$5; else if($8 ~ /del/)print $1"\t"$2"\t"$2"\t"$4"\t""-"; else if($8 ~ /ins/)print $1"\t"$2"\t"$2+(length($5))"\t"$4"\t"$5}' > Result.txt

[ShirleyDai]

No. I need to extract SNPs and Indels (some has >10 bases) as the following format:

Single nucleotide variants

chr4 150 150 A T

Insertions

Use ‘-’ in the reference_allele field and start/end coordinates must indicate the two adjacent bases in which the insertion occurs between.

chr4 150 151 - T

Deletions

Use ‘-’ in the observed_allele field to denote deletion of the given reference allele.

chr4 150 150 A -

[venu]

I've updated the answer.

[ShirleyDai]

Cool! Many Thanks.

Answer 2

[MAPK]

Why not use genomic ranges with custom R script?