Dear all,
I have to analyze a set of samples that come from a re-sequencing project.
I've been given the coordinates where the genes under analysis (those I should carry out a variant calling analysis on) are located.
Since there are reads that map spuriously to other places in the ref. genome (due to the DNA amplification process), I need to figure out a way to extract only the reads that map to the coordinates I was informed previously.
-Can anybody tell me about any tool or R package able to perform this reads filtering?
-Can the filtering step be avoided by any means (e.g. passing the coordinates to a program that would later do de variant calling without the reads filtering step).?
-Any suggestions about which software I should use to do the variant calling after that filtering (Samtools, GATK, or any other you may know about?
Thanks in advance
JL
I have to analyze a set of samples that come from a re-sequencing project.
I've been given the coordinates where the genes under analysis (those I should carry out a variant calling analysis on) are located.
Since there are reads that map spuriously to other places in the ref. genome (due to the DNA amplification process), I need to figure out a way to extract only the reads that map to the coordinates I was informed previously.
-Can anybody tell me about any tool or R package able to perform this reads filtering?
-Can the filtering step be avoided by any means (e.g. passing the coordinates to a program that would later do de variant calling without the reads filtering step).?
-Any suggestions about which software I should use to do the variant calling after that filtering (Samtools, GATK, or any other you may know about?
Thanks in advance
JL
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