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Question: Commandline Bowtie2 and variant call help.
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gravatar for syrez.m
3.0 years ago by
syrez.m • 0
syrez.m • 0 wrote:

Hello there!

When you run bowtie2 to align the reads to the genome, some stats about the file are displayed:

xxxxxx reads; of these:

  nnnnnn (f%) were unpaired; of these:

    aaaaaa (g%) aligned 0 times

    bbbbbb (h%) aligned exactly 1 time

    cccccc (j%) aligned >1 times

Can you say 'number of reads mapped' = reads aligned exactly 1 time? What's the difference?

secondly,

How do I count the number of indels in a VCF file using command line? 

Thanks!
variantcall bowtie mpileup samtools • 1.0k views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by syrez.m • 0
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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