Lollipop visualization of VCF (SnpEff output)

Question

[fifty_fifty]

I annotated WES data using SnpEff. As a result, I have an annotated vcf file. Here is an example of one line of the annotated vcf file:

chr2    15392853    .   G   A   .   PASS    AS_FilterStatus=SITE;AS_SB_TABLE=30,39|2,1;DP=73;ECNT=1;GERMQ=93;MBQ=20,41;MFRL=117,76;MMQ=60,60;MPOS=1;NALOD=1.28;NLOD=5.42;POPAF=6;TLOD=7.36;ANN=A|intron_variant|MODIFIER|ZEB1|ENSCAFG00000004023|transcript|ENSCAFT00000066606.1|protein_coding|1/8|c.59-34258C>T||||||,A|intron_variant|MODIFIER|ZEB1|ENSCAFG00000004023|transcript|ENSCAFT00000006445.6|protein_coding|1/9|c.59-34258C>T||||||,A|intron_variant|MODIFIER|ZEB1|ENSCAFG00000004023|transcript|ENSCAFT00000065928.1|protein_coding|3/10|c.10+23638C>T||||||,A|intron_variant|MODIFIER|ZEB1|ENSCAFG00000004023|transcript|ENSCAFT00000068464.1|protein_coding|1/8|c.8-34258C>T||||||,A|intron_variant|MODIFIER|ZEB1|ENSCAFG00000004023|transcript|ENSCAFT00000072100.1|protein_coding|1/7|c.59-61792C>T||||||,A|intron_variant|MODIFIE R|ZEB1|ENSCAFG00000004023|transcript|ENSCAFT00000006447.4|protein_coding|1/7|c.59-34258C>T||||||   GT:AD:AF:DP:F1R2:F2R1:FAD:SB    0/0:28,0:0.05:28:5,0:12,0:18,0:13,15,0,0    0/1:41,3:0.103:44:10,0:11,2:25,2:17,24,2,1

the fields are described here . But there is no description for the last part of the output (GT:AD:AF:DP:F1R2:F2R1:FAD:SB 0/0:28,0:0.05:28:5,0:12,0:18,0:13,15,0,0 0/1:41,3:0.103:44:10,0:11, 2:25,2:17,24,2,1)

So, this particular gene ZEB1 has 4 intron variants.

I want to visualize mutations as a lollipop plot https://github.com/pbnjay/lollipops

this method requires a gene name (TP53) and its mutations. The command looks like this:

./lollipops TP53 R273C R175H T125 R248Q

Where in my VCF file do I find mutations that look like R273C R175H T125 R248Q?

P.S.: I looked through multiple related questions with suggestions to convert vcf to maf which requires installation of VEP and vcf2maf. But I wonder if I can use Lollipop directly if I retrieve mutations in the required format from my snpeff output.

[Pierre Lindenbaum]

But there is no description for the last part of the output

this must be described in the header in the ##FORMAT lines

Answer 1

[Pierre Lindenbaum]

Where in my VCF file do I find mutations that look like R273C R175H T125 R248Q?

look in the VCF where there is a missense...

[fifty_fifty]

thank you, in my gene of interest CTNNB1 which has missense variants I found 2 mutations with HGVS.p values of p.Asp32Asn and p.Asp25Asn. The resulting lollipop plot looks like this