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（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。
WES or Panel 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
代码语言：javascript复制# ******************************************
# 1a. Mapping reads with BWA-MEM, sorting for tumor sample
# ******************************************
( sentieon bwa mem -M -R "@RGtID:$tumortSM:$tumortPL:$platform"
-t $nt -K 10000000 $fasta $tumor_fastq_1 $tumor_fastq_2 ||
echo -n 'error' ) |
sentieon util sort -o tumor_sorted.bam -t $nt --sam2bam -i -
# ******************************************
# 1b. Mapping reads with BWA-MEM, sorting for normal sample
# ******************************************
( sentieon bwa mem -M -R "@RGtID:$normaltSM:$normaltPL:$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)
代码语言：javascript复制# ******************************************
# 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)
代码语言：javascript复制# ******************************************
# 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
代码语言：javascript复制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
代码语言：javascript复制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
