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Old 12-19-2011, 05:36 AM   #1
kjaja
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Location: NY

Join Date: Aug 2011
Posts: 55
Default question about the summary statistics

Hi,

I have samples that we have exome sequence. Threse have been aligned using BWA and variants called using GATK. I would like to calculate the summary statistics across all the individuals (not for each sample )( for example, the percentage of reads aligned , the mean target coverage etc). can this be done? If so how?

Thanks,
Kay
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Old 01-11-2012, 12:01 AM   #2
Orr Shomroni
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Posts: 26
Default Two options

Have you gotten your answer in other means, Kay?

Otherwise, you can take a look at the following technique:

Code:
# Obtain depth of coverage for all target regions
/path/to/samtools depth /path/to/.bam -b /path/to/.bed > coverage_depth.tsv
# Enumerate the occuring coverage values
cut -f3 coverage_depth.tsv | sort | uniq -c | sed 's/^[ \t]*//;s/[ \t]*$//' >coverage.tsv
# Make bam file for on-target reads only
/path/to/samtools view -b /path/to/.bam -L /path/to/.bed > ontarget.bam
/path/to/samtools index /path/to/ontarget.bam
#Retrieve number of reads mapped and unmapped in ontarget files
/path/to/samtools idxstats ontarget.bam > stats_ontarget.idxstats
#Retrieve number of reads mapped and unmapped in original
/path/to/samtools idxstats /path/to/.bam  > stats_overall.idxstats
You should also check the enrichment technique offered by pfrommolt in this post:
http://seqanswers.com/forums/showthr...hlight=NGSrich
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