Created
July 30, 2019 11:01
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| rm -r genomics_db | |
| gatk GenomicsDBImport --genomicsdb-workspace-path genomics_db -L Chromosome --sample-name-map test.map --reader-threads 10 --max-num-intervals-to-import-in-parallel 10 | |
| gatk --java-options "-Xmx40g" GenotypeGVCFs -R ~/refgenome/MTB-h37rv_asm19595v2-eg18.fa -V gendb://genomics_db -O test.raw.vcf.gz | |
| bcftools view -V indels test.raw.vcf.gz | bcftools filter -e 'GT="het"' -S . | awk 'length($4)==1 || $0~/^#/' | tr '|' '/' | tr '*' '.' | bcftools view -a | bcftools view -c 1 -Oz -o test.filt.vcf.gz | |
| bcf2fasta.py test.filt.vcf.gz ~/refgenome/MTB-h37rv_asm19595v2-eg18.fa test.snps.fa |
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