Hi! I have created a project on Cancer Genomics Cloud (Simons Genome Diversity Project). Next I have downloaded SAMtools view in Apps in this project. The input file for task were : 1) The Bam file from Simons Genome Diversity Project (for example: LP6005442-DNA_B02.srt.aln.bam). As I understand the sequence is already sorted and aligned. 2) The BED region file, which contains regions of interest to me. It was download from my computer and the firs line looks like this (ch3 193593144 193697811)
There are several settings that I did not use, such as read group list, reference_file_list and others. But in my opinion it is not needed because my sequences are already aligned and sorted. As a result, I get such a filtered file, but there is no information inside file (_1_SS6004475.srt.aln.filtered.sam)
Please advise me propers settings for SAMtools
You may need to contact support for this portal to see what you may be doing wrong (unless someone here happens to have an account on that portal and can help).
On command line (which I assume you are not using, you are clicking things in a graphical user interface?) this is a simple
samtools view -L region.bed file.bam > region_file.bamcommand.