question about the summary statistics

[kjaja]

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

[Orr Shomroni]

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:

http://seqanswers.com/forums/showthread.php?t=10014&highlight=NGSrich