2.6 years ago by
For: "Can you say 'number of reads mapped' = reads aligned exactly 1 time? What's the difference?"
The number of mapped reads is the total of "aligned exactly 1 time" plus "aligned >1 times". The difference is how many times the read mapped.
It depends on the tool and the option settings, but in order to capture a mapped position the read (by itself) maps with equal statistically significant quality to each map location. This is one reason why paired-end mapping is valuable - the proximity/orientation of the two reads can help filter to find the best location (often called "concordantly mapped" or "properly paired reads" by tools/reports). The SAMTools tool group has wrapped tools to do this sort of filtering for pipelines used to call variants. For RNA-seq, some tools do the filtering as part of the tool (such as Cufflinks).
For: "How do I count the number of indels in a VCF file using command line?"
Try VCF Tools. This and other options are discussed in detail at forums like https://www.biostars.org/
Thanks, Jen, Galaxy