菜单
Assess alignment quality with coverage depth, mapping rates, insert size, and on-target metrics using samtools, mosdepth, and picard.
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基于 SOC 职业分类
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| name | genome-alignment-qc |
| description | Assess alignment quality with coverage depth, mapping rates, insert size, and on-target metrics using samtools, mosdepth, and picard. |
.bam + .bai).samtools stats and samtools flagstat for mapping summary.samtools idxstats for per-chromosome read counts.mosdepth for coverage distribution (genome-wide, or restricted to target BED).picard CollectInsertSizeMetrics for insert size distribution.picard CollectAlignmentSummaryMetrics for detailed alignment statistics.knowledge/sources/genomics/quality-thresholds.md).samtools stats and samtools flagstat output files.mosdepth coverage files (.mosdepth.global.dist.txt, .per-base.bed.gz if enabled).$PATH..bai) missing or out of date relative to the BAM file.chr1 vs 1)..dict).