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http://gatkforums.broadinstitute.org/gatk/discussion/6019/what-is-firepony-and-what-can-i-expect-from-it
https://github.com/broadinstitute/firepony
https://github.com/broadinstitute/firepony/wiki
h…
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Hi Qing,
As you said in Issues #21 , multi-mapping to a combined alignments and strict criterion were used to get the real SNVs and these can be replaced by other methods such as GATK. So should I ru…
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Is there a reason you use GATK 3.5 instead of the latest 4.1?
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bwa command line from GATK: `bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta`
bwa mem reference page: https://bio-bwa.sourceforge.net/bwa.shtml
What the options mean:
```
-K: minimum seed len…
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MergeGVCFs and ploidy = 1 seems to make the GATK hang.
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### Summary
A user wrote in to the forum regarding running FilterSamReads through GATK and the output bam file has formatting issues. After they sent in a bug report, I found that the exit code is g…
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Hi,
Thank you for an awesome tool. Great that have a replacement for Contest and VerifyBAMID.
My question is whether you had a chance to test it with GATK 4. GATK4 has a different command line i…
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Hi,
What are your plans for supporting GATK 4.0?
Thanks,
Ted
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``` // GATK_SELECT_VARIANTS__INTERVALS(GATK_INDEX_FEATURE_FILE.out, params.drgenes_list)``` in the CALL workflow is not yet enabled, is the ``` -L ${intervalsFile} \\``` available yet? Or should I cr…
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Hello Alex,
I want to detect germline variant using GATK as it's described in this pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indel…