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