SnpSift command query

Question

[prasundutta87]

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?

Answer 1

[Pierre Lindenbaum]

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

[prasundutta87]

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?

Answer 2

[Robert Sicko]

&& 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

[prasundutta87]

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 '|'.

[Robert Sicko]

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