体细胞突变检测分析流程-系列1（ WES&Panel）

标签：体细胞 tumor sentieon normal -- WES bam filter Panel

Sentieon●体细胞变异检测-系列1

  Sentieon 致力于解决生物信息数据分析中的速度与准确度瓶颈，通过算法的深度优化和企业级的软件工程，大幅度提升NGS数据处理的效率、准确度和可靠性。   针对体细胞变异检测，Sentieon软件提供两个模块：TNscope和TNhaplotyer2。   TNscope：此模块使用Sentieon特有的算法，拥有更快的计算速度和更高的计算精度，对临床基因诊断样本尤其适用；   TNhaplotyper2：此模块匹配Mutect2（现在匹配到4.1.9）结果的同时，计算速度提升10倍以上。  

WES or Panel 变异检测分析

 

以下给出的步骤脚本主要针对WES or Panel (200~500x depth, AF > 1%)。（查看脚本时，可以左右滑动）

 

第一步：Alignment

# ****************************************** 
# 1a. Mapping reads with BWA-MEM, sorting for tumor sample 
# ****************************************** 
( sentieon bwa mem -M -R "@RG\tID:$tumor\tSM:$tumor\tPL:$platform" \
-t $nt -K 10000000 $fasta $tumor_fastq_1 $tumor_fastq_2 || \
echo -n 'error' ) | \
sentieon util sort -o tumor_sorted.bam -t $nt --sam2bam -i -

# ****************************************** 
# 1b. Mapping reads with BWA-MEM, sorting for normal sample 
# ****************************************** 
( sentieon bwa mem -M -R "@RG\tID:$normal\tSM:$normal\tPL:$platform" \
-t $nt -K 10000000 $fasta $normal_fastq_1 $normal_fastq_2 || 
echo -n 'error' ) | \
sentieon util sort -o normal_sorted.bam -t $nt --sam2bam -i -

 

第二步：PCR Duplicate Removal (Skip For Amplicon)

# ****************************************** 
# 2a. Remove duplicate reads for tumor sample. 
# ****************************************** 
# ******************************************  
sentieon driver -t $nt -i tumor_sorted.bam \
      --algo LocusCollector \
      --fun score_info \ tumor_score.txt sentieon driver -t $nt -i tumor_sorted.bam \
      --algo Dedup \
      --score_info tumor_score.txt \
      --metrics tumor_dedup_metrics.txt \ tumor_deduped.bam
# ****************************************** 
# 2b. Remove duplicate reads for normal sample. 
# ****************************************** 
sentieon driver -t $nt -i normal_sorted.bam \
     --algo LocusCollector \
     --fun score_info \ normal_score.txt sentieon driver -t $nt -i normal_sorted.bam \
     --algo Dedup \
     --score_info normal_score.txt \
     --metrics normal_dedup_metrics.txt \ normal_deduped.bam

 

第三步: Base Quality Score Recalibration (Skip For Small Panel)

# ****************************************** 
# 3a. Base recalibration for tumor sample
# ******************************************
sentieon driver -r $fasta -t $nt -i tumor_deduped.bam --interval $BED \
    --algo QualCal \
    -k $dbsnp \
    -k $known_Mills_indels \
    -k $known_1000G_indels \ tumor_recal_data.table
# ****************************************** 
# 3b. Base recalibration for normal sample 
# ****************************************** 
sentieon driver -r $fasta -t $nt -i normal_deduped.bam --interval $BED \
     --algo QualCal \
     -k $dbsnp \
     -k $known_Mills_indels \
     -k $known_1000G_indels \ 
     normal_recal_data.table

 

第四步：Variant Calling

sentieon driver -r $fasta -t $nt -i tumor_deduped.bam -i normal_deduped.bam --interval $BED -interval_padding 10\ 
    --algo TNscope \
    --tumor_sample $TUMOR_SM \
    --normal_sample $NORMAL_SM \
    --dbsnp $dbsnp \
    --sv_mask_ext 10 \
    --max_fisher_pv_active 0.05 \
    --min_tumor_allele_frac 0.01 \
    --filter_t_alt_frac 0.01 \
    --max_normal_alt_frac 0.005 \
    --max_normal_alt_qsum 200 \
    --max_normal_alt_cnt 5 \
    --assemble_mode 4 \
    [--pon panel_of_normal.vcf \] 
    output_tnscope.pre_filter.vcf.gz

 

第五步：Variant Filtration

bcftools annotate -x "FILTER/triallelic_site" output_tnscope.pre_filter.vcf.gz | \ 
    bcftools filter -m + -s "insignificant" -e "(PV>0.25 && PV2>0.25)" | \ 
    bcftools filter -m + -s "insignificant" -e "(INFO/STR == 1 && PV>0.05)" | \ 
    bcftools filter -m + -s "orientation_bias" -e "FMT/FOXOG[0] == 1" | \ 
    bcftools filter -m + -s "strand_bias" -e "SOR > 3" | \ 
    bcftools filter -m + -s "low_qual" -e "QUAL < 20" | \ 
    bcftools filter -m + -s "short_tandem_repeat" -e "RPA[0]>=10" | \
    bcftools filter -m + -s "noisy_region" -e "ECNT>5" | \ 
    bcftools filter -m + -s "read_pos_bias" -e "FMT/ReadPosRankSumPS[0] < -8" | \ 
    bcftools norm -f $fasta -m +any | \ 
sentieon util vcfconvert - output_tnscope.filtered.vcf.gz

标签：体细胞,tumor,sentieon,normal,--,WES,bam,filter,Panel
From： https://www.cnblogs.com/chsnp/p/17523107.html