For each position, Thanks, I will search PanDepth
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Michelle Guerra •
DEPTH IN GBS
Hi all! I need help, I have files from GBS and need to know your depth of files. I know it is necessary “samtools depth”, but I do not know the difference between using Flags (-a) or not using it. Because it is important to consider zero positions. You help me.
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cmdcolin
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written
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Michelle Guerra •
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Michelle Guerra •
1 answer
I'm not quite sure if you are looking for depth data for each position (including zero positions) or specific regions. If you have a large amount of GBS data and wish to calculate the coverage or depth for each sample, you can try PanDepth, a specialized tool for coverage and depth calculation that supports both short reads and long reads.
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why did I get 0 at the 3rd column with samtools depth?
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what don't you understand here ?
Is it important to consider zero positions?
yes. but there are better tools than samtools depth to get the depth. e.g: mosdepth.