Question: SnpSift command query
0
gravatar for prasundutta87
8 days ago by
prasundutta870 wrote:

Hi,

I wish to exclude all the variants in a vcf file where the first snpeff annotation is either intron_variant or 'splice_acceptor_variant&intron_variant or 'splice_region_variant&intron_variant' or 'splice_donor_variant&intron_variant.

Now the command that does NOT work is:

java -jar SnpSift.jar filter "(ANN[0].EFFECT != 'intron_variant')|(ANN[0].EFFECT !='splice_acceptor_variant&intron_variant')|(ANN[0].EFFECT !='splice_region_variant&intron_variant')|(ANN[0].EFFECT != 'splice_donor_variant&intron_variant')" final_result.vcf >final_result_no_introns.vcf

The above command works when I replace '|' with '&&'.

Is this a software issue or I am not understanding the usage of the logical operators in SnpSift correctly?

snp software error • 99 views
ADD COMMENTlink modified 8 days ago by Robert Sicko460 • written 8 days ago by prasundutta870
1
gravatar for Pierre Lindenbaum
8 days ago by
France
Pierre Lindenbaum89k wrote:

try '||' (OR operator) instead of '|' (bitwise inclusive OR operator)

ADD COMMENTlink written 8 days ago by Pierre Lindenbaum89k

Thank you for the suggestion. I used it just now. No filtering was performed on my input file..furthermore the operator '&&' doing the job does not make sense. Is there a catch somewhere that I am missing?

ADD REPLYlink modified 8 days ago • written 8 days ago by prasundutta870
1
gravatar for Robert Sicko
8 days ago by
Robert Sicko460
United States
Robert Sicko460 wrote:

&& makes sense if you are using annotation !=

you want to keep variants where the first annotation != 'intron_variant' AND first annotation != 'splice_acceptor_variant&intron_variant' AND first annotation != 'splice_region_variant&intron_variant' AND first annotation != 'splice_donor_variant&intron_variant'

= left with variants where first annotation != any of the above

ADD COMMENTlink written 8 days ago by Robert Sicko460

Actually since | is the OR operator, if any one condition is TRUE, then only filtering will take place.

When && or AND operator is used, it means that if all the conditions are TRUE together, only then filtering will take place. Since, one variant willl have only one effect in the first annotation, I used '|'.

ADD REPLYlink modified 6 days ago • written 6 days ago by prasundutta870

Right, but I believe snpsift filter keeps variants that pass the specified condition(s) rather than filter variants that do not pass the specified condition(s). Look at the examples given on the snpsift filter documentation page

ADD REPLYlink written 4 days ago by Robert Sicko460
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