snippy

软件结果：

 

• 先得到raw snp

        ### freebayes-parallel reference/ref.txt 8 -p 1 -q 20 -m 60 --min-coverage 10 -V -f reference/ref.fa snp.bam > snp.raw.vcf

 

• 然后用filter 过滤掉了质量差的

        ### /ldfssz1/ST_INFECTION/F16ZQSB1SY3030_Salmonella/USER/lindechun/software/snippy/bin/snippy-vcf_filter --minqual 10 --mincov 10 --minfrac 0.9  snp.raw.vcf > snp.filt.vcf 

        Parsing: snp.raw.vcf

        Types: ins=224 snp=25637 mnp=401 complex=2689 del=304

        Passed 29255/30761 variants (95.10%)

 

• 注释信息

        ### snpEff ann -no-downstream -no-upstream -no-intergenic -no-utr -c reference/snpeff.config -dataDir . -noStats ref snp.filt.vcf > snp.vcf

 

• Only keep equal length alleles

        ###/software/snippy/bin/snippy-vcf_filter --subs snp.filt.vcf > snp.filt.subs.vcf 2>> snp.log