MINQ error in extractHAIRS step

[JYLeeBioinfo]

Hi

I am trying to phase SVs using Nanopore data

I encountered the following error.

MINQ must be at least 4

So I added --ONT 1 to the following command in the src/crossstitch.sh

(original)
$EXTRACTHAIRS --mbq 0 --bam $LONGREADSBAM --VCF $PHASEDSNPS.prehairs --out $OUTPREFIX.hairs

(changed)
$EXTRACTHAIRS --mbq 0 --bam $LONGREADSBAM --VCF $PHASEDSNPS.prehairs --out $OUTPREFIX.hairs --ONT 1

All processes finished well after changed it.

Is it okay to add ONT option to extractHAIRs step?

[mschatz]

We haven’t tested it but should be okay

Good luck

Mike

On Jun 22, 2019, at 11:52 AM, hd00ljy notifications@github.com wrote:

Hi

I am trying to phase SVs using Nanopore data

I encountered the following error.

MINQ must be at least 4 So I added --ONT 1 to the following command in the src/crossstitch.sh

(original) $EXTRACTHAIRS --mbq 0 --bam $LONGREADSBAM --VCF $PHASEDSNPS.prehairs --out $OUTPREFIX.hairs

(changed) $EXTRACTHAIRS --mbq 0 --bam $LONGREADSBAM --VCF $PHASEDSNPS.prehairs --out $OUTPREFIX.hairs --ONT 1 All processes finished well after changed it.

Is it okay to add ONT option to extractHAIRs step?

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[JYLeeBioinfo]

Thank you Mike!

[JYLeeBioinfo]

It seems I have to add reference if I add --ONT 1