Question: SnpSift command query
0
gravatar for prasundutta87
5 months 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 • 265 views
ADD COMMENTlink modified 5 months ago by Robert Sicko470 • written 5 months ago by prasundutta870
1
gravatar for Pierre Lindenbaum
5 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum96k wrote:

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

ADD COMMENTlink written 5 months ago by Pierre Lindenbaum96k

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 5 months ago • written 5 months ago by prasundutta870
1
gravatar for Robert Sicko
5 months ago by
Robert Sicko470
United States
Robert Sicko470 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 5 months ago by Robert Sicko470

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 5 months ago • written 5 months 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 5 months ago by Robert Sicko470
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