How can you convert a GATK interval_list file into a BED file

Question

[mark.fleharty]

I'm trying to convert an interval list into a BED file, any ideas on how to do it?

Thanks,
Mark

Answer 1

[Zaag]

From file test.interval

sed 's/:\|-/\t/gi' test.interval > test.bed

[kianalee]

Hello, I am having the same issues as the individual who originally posted. I tried using the command you provided and then inputting into the UCSC liftover tool, but I received an error that the BED format was incorrect. Do you have any other suggestions on how to convert a GATK .interval_list into BED format?

[from the mountains]

you can try

sed 's/:\|-/\t/gi' test.interval | grep -v "^@" | cut -f 1-3 > test.bed

at the end of the day the only requirement is to satisfy what's here: https://m.ensembl.org/info/website/upload/bed.html so columns 1-3 is just the bare minimum.

Answer 2

[mark.fleharty]

It appears that Picard has a tool to do the opposite of what I'd like to do.

http://broadinstitute.github.io/picard/command-line-overview.html#BedToIntervalList

[Zaag]

Do you mean GATK interval list or Picard interval list?