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Old 12-19-2011, 06:36 AM   #1
Location: NY

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


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?

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Old 01-11-2012, 01:01 AM   #2
Orr Shomroni
Location: Netherlands

Join Date: Oct 2011
Posts: 26
Default Two options

Have you gotten your answer in other means, Kay?

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

# 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:
"Though it may seem that all's been said and done, originality still lives on" - some unoriginal guy who had nothing better to write as his signature
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