bedsFromBAMsForGEO.zip

Filtering of alignments for ichorCNA and fragmentomic analysis. Samtools (Version 1.9) was used to filter BAM alignments, unmapped reads, secondary and supplementary reads, reads with Minimap2 mapping quality less than 20 as in https://doi.org/10.1101/2020.12.28.424602, and reads longer than 700bp. Bedtobam was used to create bed files. All genomic coordinates are in GRCh38.

针对ichorCNA与片段组学分析的比对结果过滤流程。使用Samtools（版本1.9）过滤BAM格式比对文件，具体过滤内容包括未比对读段、次级比对与补充比对读段、经Minimap2比对得到的质量值低于20的读段，以及长度超过700bp的读段，相关操作参照文献https://doi.org/10.1101/2020.12.28.424602。使用Bedtobam工具生成BED格式文件。所有基因组坐标均采用GRCh38参考基因组版本。