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Hi,
I have a human sequencing data, and reads have been mapped with bwa. Any suggestions on what is the best way to extract following statistics? I tried samtools, but it seems it is hard to output exactly what I need. I am wondering if GATK or other varient detector would make the job easier here. Thanks
For each predicted variant, I would like to extract information about 1) #the number of reads with predicted variant on + and - strand respectively 2) #average variant location for reads with predicted SNP
I have a human sequencing data, and reads have been mapped with bwa. Any suggestions on what is the best way to extract following statistics? I tried samtools, but it seems it is hard to output exactly what I need. I am wondering if GATK or other varient detector would make the job easier here. Thanks
For each predicted variant, I would like to extract information about 1) #the number of reads with predicted variant on + and - strand respectively 2) #average variant location for reads with predicted SNP
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