今日看点：加速体细胞突变检测分析流程-系列2（ctDNA等高深度样本）

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今日看点：加速体细胞突变检测分析流程-系列2（ctDNA等高深度样本）

2023-07-05 15:55:16 来源：博客园

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Sentieon●体细胞变异检测系列-2

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（提速10倍+）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。

ctDNA变异检测分析

以下给出的步骤脚本，主要针对ctDNA和其他高深度测序的样本数据(2000-5000x depth, AF > 0.3%)

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 (Tumor Only)

sentieon driver -r $fasta -t $nt -i tumor_deduped.bam --interval $BED --interval_padding 10 \     --algo TNscope \     --tumor_sample $TUMOR_SM \     --dbsnp $dbsnp \     --disable_detector sv \     --min_tumor_allele_frac 3e-3 \     --filter_t_alt_frac 3e-3 \     --clip_by_minbq 1 \     --min_init_tumor_lod 3.0 \     --min_tumor_lod 3.0 \     --assemble_mode 4 \     --resample_depth 100000 \     [--pon panel_of_normal.vcf \]      output_tnscope.pre_filter.vcf.gz

第五步：Variant Filtration (Tumor Only)

bcftools annotate -x "FILTER/triallelic_site" output_tnscope.pre_filter.vcf.gz | \    bcftools filter -m + -s "low_qual" -e "QUAL < 10" | \    bcftools filter -m + -s "short_tandem_repeat" -e "RPA[0]>=10" | \    bcftools filter -m + -s "read_pos_bias" -e "FMT/ReadPosRankSumPS[0] < -5" | \   bcftools norm -f $fasta -m +any | \ sentieon util vcfconvert - output_tnscope.filtered.vcf.gz

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