bcftools isec -n operators
I am still very confused by the use of the bcftools isec -n flag.
According to the manual: https://samtools.github.io/bcftools/bcftools.html#isec):
-n, --nfiles [+-=]INT|~BITMAP
output positions present in this many (=), this many or more (+), this many or fewer (-), or the exact same (~) files
But after a few trials, I have realized that -n+2 and -n=10 with an input of 10 files do not output the same results.
Has anyone any clues about the use of these operator?
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Of course not.
-n+2translates to "present in 2 or more among the 10 files".-n=10translates to "present in all 10 files". Why do you expect them to have the same results?Thank you RamRS, I simply had not understood the correct function of the operator.
So, to reformulate, in a command with 10 files:
-n+2translates "variants present in 2 or more files among the 10 files" or "all the variants that are in at least 2 files"-n=2translates "variants present in exactly 2 files among the 10 files"-n-2translates "variants present in 2 or less files among the 10 files" or "variants not shared by more than 2 files"-n~2translates "the variants that are altogether shared by 2 files among the 10 files"Is it correct?
I think I am still a bit confused by the operator ~
The
~operator is used with aBITMAP, not theINTpart. The example given in the section shows how it can be used. If you have a bunch of files (10 in your case), and you wish to say not only how many files, but also which files the entry should be a part of, you can use the~operator.Find all entries present in 5 files:
-n=5Find all entries present in the 2nd, 3rd, 6th, 7th and 9th files:
-n~0110011010(see how the 1s denote the files to be used)Thanks a lot RamRS, it is very clear now!
It would be handy to have the very same example you have provided in the bcftools manual.
There is a better example in there:
@Ram Clear and Concise. Thanks for the comment!