SNP calling

SNP calling

0

Hello

I made for 83 samples bam file a vcf file with HaplotypeCaller then filtered with VarianFiltration, after that with vcfR package in R program got “GT”. but I have many no-call (./.). I want to remove no-call .

also I used of gatk HaplotypeCaller -R reference.fasta -I sample1.bam -O variants.g.vcf -ERC GVCF to made a variants.g.vcf , becuaase variants.g.vcf is need as input file for GenotypeGVCFs, but I have second problem, for 83 bam files, I had error to make a variants.g.vcf . “A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode currently. Use the –sample-name argument to run on a single sample out of a multi-sample BAM file.”

May give me some suggestion?
thank you


SNPcalling

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