Is there samtools that give a location in genome that has multiple reads covering that region?
Pretty new to pysam and for my project I have to write something that provides a location that maps to multiple reads covering that region but have not been able to find this in the documentation. Does anyone know if samtools can provide this or what other methods can be used to get the location in genome?
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GenoMax
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catherinesac07 •
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catherinesac07 •
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Check samtools depth.
samtools depth [options] in1.bam [in2.bam [...]]
The output is a simple tab-separated table with three columns: reference name, position, and coverage depth. Note that positions with zero coverage may be omitted by default; see the -a option.
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