Hi, I am currently using samtools version 1.3 (using htslib 1.3). When I calculate the depth for each gene specified with position in a .txt file like this, 3:5291-7456 3:10145-12620 3:45132-50806 3:488560-496174 3:502975-509286 3:514953-518821 3:519555-527018 3:519611-521867 3:539149-544309 3:548633-552697
It all goes fine until when I reach some point and all the following did not work. samtools depth -a -r 3:559148481-559151843 LIB_3.bam then I also tried to view it, it did not work neither samtools view 1839_LIB21703_LDI18976_CCGTCC_L003-trimmed-pair_sorted_mdup.bam 3:559148481-559151843 However when I use following, it shows there are reads mapped here, properly paired with good mapping quality samtools view LIB21688_3H_filtered_sorted_mdup.bam | awk '$4>559148481&&$4<559151843' anyone knows what is the problem here? why does samtools won't calculate here? PS after BWA mapping, I extract one chromosome and filtered out unmapped and secondary alignment, I did sorting and marking duplicates and indexing. Best regards, Qiongxian
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