could anyone please explain how to count # of SNPs in 454HCDiffs file?
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If memory serves me correctly each SNP has a header line starting with a >, so:
grep -e "^>" 454HCDiffs.txt | wc -l
Should do the trick. -
You should bear in mind that this would count indels as well as SNPs.Comment
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many thanks nickloman,
However it would be thankful if I could count each type separately (SNPs & INDELs).
regards,Comment
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OK, well you could do something like this to count SNPs:
grep -e "^>" 454HCDiffs.txt | awk '($4 ~ /^[ATGC]$/ && $5 ~ /^[ATGC]$/)' | wc -l
The difference between that and the previous recipe will be the indels.Comment
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Thanks nickloman, I really appreciate your help.
best,Comment
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