I think there is a bug when parsing insertions in reverse complement genes only. I've made a VCF file attached with an insertion/deletion in forward/reverse genes. They are all near the start of each gene to make life a bit easier.
insertion in forward, rpoB
We aim to insert three bases after the 4th base (759810, g) and before the 5th base (759811,c) hence encode in VCF as
NC_000962.3 759810 . G GTCG
and this is reported correctly as 759810_ins_tcg in variants and 4_ins_tcg in mutations.
insertion in reverse, pncA
To insert three bases after the 4th base (2289238, c) in a reverse complemented gene, we have to insert three bases after the 5th base (2289237, g) like
NC_000962.3 2289237 . C CTCG
and this is reported correctly as 2289237_ins_tcg in variants but rather than get the expected 4_ins_cga in mutations we get instead 5_ins_cga.
deletion in forward, gyrA
To delete the 4th and 5th bases, we specify the 3rd base and then drop the 4th and 5th in the ALT column. Hence for gyrA this is
NC_000962.3 7305 . ACA A
and this is reported correctly as 7306_del_ca in variants but incorrectly in mutations as 5_del_ca rather than the expected 4_del_ca.
deletion in reverse gene, katG
We aim to delete the 4th and 5th bases. BUT because the VCF talks forward strand we need to structure this as starting at the 6th base (which is upstream and a c on the reverse strand) and delete the "next" two bases i.e.
NC_000962.3 2156106 . GGG G
this is correctly reported as 2156107_del_gg and in mutations is correctly reported as 4_del_cc.
I think there is a bug when parsing insertions in reverse complement genes only. I've made a VCF file attached with an insertion/deletion in forward/reverse genes. They are all near the start of each gene to make life a bit easier.
insertion in forward, rpoB
We aim to insert three bases after the 4th base (759810, g) and before the 5th base (759811,c) hence encode in VCF as
and this is reported correctly as
759810_ins_tcg
in variants and4_ins_tcg
in mutations.insertion in reverse, pncA
To insert three bases after the 4th base (2289238, c) in a reverse complemented gene, we have to insert three bases after the 5th base (2289237, g) like
and this is reported correctly as
2289237_ins_tcg
in variants but rather than get the expected4_ins_cga
in mutations we get instead5_ins_cga
.deletion in forward, gyrA
To delete the 4th and 5th bases, we specify the 3rd base and then drop the 4th and 5th in the
ALT
column. Hence for gyrA this isand this is reported correctly as
7306_del_ca
in variants but incorrectly in mutations as5_del_ca
rather than the expected4_del_ca
.deletion in reverse gene, katG
We aim to delete the 4th and 5th bases. BUT because the VCF talks forward strand we need to structure this as starting at the 6th base (which is upstream and a
c
on the reverse strand) and delete the "next" two bases i.e.this is correctly reported as
2156107_del_gg
and in mutations is correctly reported as4_del_cc
.Can test with VCF and catalogue attached.
test_004.zip