Hi Everyone. I've googled long and hard for this, as well as trying every parameter that I can think of, but my indel detection pipeline is only picking up SNPs.
I know this because I introduced 104 copies of an artificially created insertion and 104 copies of an artificial deletion, which are present in my SAM file.
The relevant section of my pipeline is as follows (just a bash script):
Unfortunately there are no entries marked as INDEL in the resulting VCF file.
Any suggestions as to what I might be doing wrong would be most welcome!
Thanks for reading.
Cameron
I know this because I introduced 104 copies of an artificially created insertion and 104 copies of an artificial deletion, which are present in my SAM file.
The relevant section of my pipeline is as follows (just a bash script):
Code:
$TOOLS/samtools mpileup -E -C50 -g -e15 -o30 -F0.005 -P ILLUMINA -uf $INDEX $SAM.sorted.bam > $SAM.bcf $TOOLS/bcftools view -vcg -i0.001 $SAM.bcf > $SAM.vcf cat $SAM.vcf | grep "INDEL" > $SAM.indels.vcf
Any suggestions as to what I might be doing wrong would be most welcome!
Thanks for reading.
Cameron
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