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

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

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

Thanks,
Mark

bed interval-list gatk

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updated 3.6 years ago by Ram

• written 11.2 years ago by mark.fleharty •

2 answers

From file test.interval

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

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updated 6.8 years ago by Ram

• written 11.2 years ago by Zaag

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?

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written 7.0 years ago by kianalee •

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.

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written 6.2 years ago by from the mountains

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

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updated 6.8 years ago by Ram

• written 11.2 years ago by mark.fleharty •

Do you mean GATK interval list or Picard interval list?

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written 11.2 years ago by Zaag

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