Question

How to call variants using BBMap, if possible with charts and graphics?

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7.8 years ago

human_genomeXXX ▴ 10

I run bbmap.sh in=0001.fastq in2=0002.fastq out=bbmap_mapped.sam ref=H37Rv_reference.fa # indexing and aligning in paired mode

callvariants.sh=bbmap_mapped.sam ref=H37Rv_reference.fa out=BBMap_variant_call.vcf # this line can`t find .sh script

though bbmap in echo $PATH

How to fix that?

thank you

bbmap variant calling • 3.3k views

ADD COMMENT • link updated 7.8 years ago by Brian Bushnell 20k • written 7.8 years ago by human_genomeXXX ▴ 10

score 1 · Answer 1 · 2017-02-02

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7.8 years ago

Brian Bushnell 20k

callvariants.sh=bbmap_mapped.sam ref=H37Rv_reference.fa out=BBMap_variant_call.vcf

should be:

callvariants.sh in=bbmap_mapped.sam ref=H37Rv_reference.fa out=BBMap_variant_call.vcf

ADD COMMENT • link 7.8 years ago by Brian Bushnell 20k

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What about the chart and the graphics part :)

ADD REPLY • link 7.8 years ago by GenoMax 147k

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And I want a pony!

You guys are more patient/polite than I am, esp. given the OP's thread on GATK variant calling (although @WouterDeCoster did resort to RTFM).

ADD REPLY • link 7.8 years ago by harold.smith.tarheel ★ 5.0k

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Nothing wrong with a fantastic manual amirite?

ADD REPLY • link 7.8 years ago by WouterDeCoster 47k

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The manual apparently doesn't suffice. I hope Brian has time to go over to OP in person to sort this out and sit next to him when he attempts commands.

ADD REPLY • link 7.8 years ago by WouterDeCoster 47k

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So, I'm crowdsourcing an instructional video, and look for donations and actors... anyone? :)

ADD REPLY • link 7.8 years ago by Brian Bushnell 20k

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I can donate an actor.

ADD REPLY • link 7.8 years ago by WouterDeCoster 47k

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thank you, you have developed an outstanding tools, could you please advise how to preprocess the resultant VCFs and annotate it? Is there any better substitution of SNPEff and ClinEff?