2022-05-13 碱基质量重校正时遇到的gatk-bundle下载vcf文件问题

一、问题

在按照GATK流程做碱基质量重校正时，需要用到gatk-bundle中下载的一些已知位点vcf文件，如：

• resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf
• resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf
• resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf
  但是在运行下述脚本时，提示--known-sites这里存在错误。

ref_genome_fasta_file=~/database/ref_genome/human/hg38/gatk-bundle/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta
dbsnp=~/database/ref_genome/human/hg38/gatk-bundle/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf
Mills_1000G_indel=~/database/ref_genome/human/hg38/gatk-bundle/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
assembly38_indel=~/database/ref_genome/human/hg38/gatk-bundle/resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz

#### BQSR
    echo "Start ${i} BQSR for ${id}." `date`
    $GATK --java-options "-Xmx10G -Djava.io.tmpdir=./${dir}/tmp"  BaseRecalibrator \
          -R ${GENOME}                  \
          -I ./${dir}/${id}_markdup.bam \
          --known-sites ${dbsnp}        \
          --known-sites ${Mills_1000G_indel} \
          --known-sites ${assembly38_indel}  \
          -O ./${dir}/${id}_BaseRecal.table \
          1>./${dir}/${id}_BaseRecal.log 2>&1
    echo -e "BQSR for ${id} has finised at:" `date` "\n"

二、解决方法

参考该帖后，发现原因是因为gatk-bundle下载的vcf文件是二进制的，需要先用bcftools处理一下就可以正确运行BQSR了。

bcftools view -O z -o tmp.vcf.gz resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf
mv tmp.vcf.gz resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
bcftools index -t resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz

bcftools view -O z -o tmp.vcf.gz resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf
mv tmp.vcf.gz resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz
bcftools index -t resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz