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Merge vcf files should be enhanced #1

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xiucz opened this issue Jul 22, 2019 · 0 comments
Open

Merge vcf files should be enhanced #1

xiucz opened this issue Jul 22, 2019 · 0 comments

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@xiucz
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xiucz commented Jul 22, 2019

Other vcf files like freebayes output files should be merged, like the tool CombineVariants in gatk did:

java -jar ~/gatktools/GenomeAnalysisTK.jar -T CombineVariants \
-R ~/database/hg19/gatk_bundle/ucsc.hg19.fasta \
-genotypeMergeOptions UNIQUIFY -priority VQSR,freebayes \
-V:VQSR MergeVcfs.vcf \
-V:freebayes freebayes.filter.results.vcf \
-o germline.integrated.vcf

Thank you,
Xiucz.
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