chapter4.md

第四章 变异过滤

{:toc}

GATK的过滤

$ MEANQUAL=$(awk '{ if ($1 !~ /#/) { total += $6; count++  }  } END { print total/count  }' sample.concordance.raw.vcf)
$ java  -jar GenomeAnalysisTK.jar \
        -R ref.fa \
        -T VariantFiltration \
        --filterExpression "QD < 20.0 || ReadPosRankSum < -8.0 || FS > 10.0 || QUAL < $MEANQUAL" --filterName LowQualFilter \
        --missingValuesInExpressionsShouldEvaluateAsFailing \
        --variant sample.concordance.raw.vcf \
        --logging_level ERROR -o sample.concordance.flt.vcf \
        -log ./log/sample.concordance.flt.vcf.log
$ grep -v "Filter" sample.concordance.flt.vcf > sample.concordance.flt.knowsites.vcf

变异检测

关于SNP的过滤（1）：如何使用vcftools进行SNP过滤

来自 <https://www.jianshu.com/p/e05ff3cace56?utm_campaign=maleskine&utm_content=note&utm_medium=seo_notes&utm_source=recommendation>

关于SNP的过滤（2）：如何使用vcftools进行SNP过滤

来自 <https://cdn2.jianshu.io/p/52b2dcb601d2>