samtools格式转换报错-linux013

samtools报错

[mem_sam_pe] paired reads have different names: "LH00T36", "LH00380:121:2253W5LT4:8:1397:11779:5006" [mem_sam_pe] paired reads have different names: "LH00380:121:2253W5LT4:8:1397:21991:4978", "LH00380:121:2253W5LT4:8:1397:12475:5006" [W::sam_read1_sam] Parse error at line 25257000 samtools view: error reading file "-" [bam_sort_core] merging from 0 files and 30 in-memory blocks...

由于使用了错误的文件传输导致不能识别比对数据，产生了比对冗余错乱

view的错误

cat X |  | samtools view -h -F 4 | samtools sort -@ 30 -O BAM  -o sampleX_sorted.bam

改为

cat X |  | samtools view -S -b - > newX.bam

Samtools安装与使用-samtools-v1.17（bioinfomatics tools-007）-****博客