Merge pull request #201 from ggabernet/freebayes

Freebayes germline

CHANGELOG.md

@@ -24,7 +24,7 @@ Piellorieppe is one of the main massif in the Sarek National Park.
 - [#174](https://github.com/nf-core/sarek/pull/174) - Add `variant_calling.md` documentation
 - [#175](https://github.com/nf-core/sarek/pull/175) - Add `Sentieon` documentation
 - [#176](https://github.com/nf-core/sarek/pull/176) - Add empty `custom` genome in `genomes.config` to allow genomes that are not in `AWS iGenomes`
-- [#179](https://github.com/nf-core/sarek/pull/179) - Add `FreeBayes` germline variant calling
+- [#179](https://github.com/nf-core/sarek/pull/179), [#201](https://github.com/nf-core/sarek/pull/201) - Add `FreeBayes` germline variant calling
 - [#180](https://github.com/nf-core/sarek/pull/180) - Now saving Mapped BAMs (and creating TSV) in minimal setting
 - [#182](https://github.com/nf-core/sarek/pull/182) - Add possibility to run `HaplotypeCaller` without `dbsnp` so it can be used to actually generate vcfs to build a set of known sites (cf [gatkforums](https://gatkforums.broadinstitute.org/gatk/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x))
 - [#195](https://github.com/nf-core/sarek/pull/195) - Now creating TSV for duplicates marked BAMs in minimal setting

main.nf

@@ -2192,14 +2192,8 @@ process FreebayesSingle {
     """
     freebayes \
         -f ${fasta} \
-        --pooled-continuous \
-        --pooled-discrete \
-        --genotype-qualities \
-        --report-genotype-likelihood-max \
-        --allele-balance-priors-off \
-        --min-alternate-fraction 0.03 \
-        --min-repeat-entropy 1 \
-        --min-alternate-count 2 \
+        --min-alternate-fraction 0.1 \
+        --min-mapping-quality 1 \
         ${intervalsOptions} \
         ${bam} > ${intervalBed.baseName}_${idSample}.vcf
     """