customProDB: "complex" SNV scenarios handling
1
0
Entering edit mode
iranmdl15 • 0
@iranmdl15-17167
Last seen 4.2 years ago

Hello all!

I am about using customProDB for the first time and I have several questions regarding the package functionalities:
1) Does customProDB accept phased VCF file and produce accordingly the different protein products from each allele depending on the phase in the VCF file?
2) How does customProDB treat multiple variants affecting to a single amino acid (single codon)? Let's say that we have 2 non-synonymous variants at different positions of a given codon.

Thank you in advance,

customprodb • 545 views
ADD COMMENT
0
Entering edit mode
@xiaojingwang-8081
Last seen 4.3 years ago
United States
1)            No. We use the VCF file to generate a protein FASTA file with variations. You will need a simple script to parse two FASTA files (a regular one downloaded from ucsc and the one generated from vcf file) into one with the 1/1, 0/1 information in vcf file. 2)            This is a complicated question. There are two scenarios. a). two SNVs are present on the same read. b). Two SNVs are present on different reads. With limited information in vcf file, it is difficult to tell which scenario it is. Therefore, we treat each SNVs as independent ones. Thanks, Xiaojing From: "iranmdl15 [bioc]" <noreply@bioconductor.org> Reply-To: <reply+aab215a7+code@bioconductor.org> Date: Tuesday, September 4, 2018 at 5:01 AM To: <xwang.research@gmail.com> Subject: [bioc] customProDB: "complex" SNV scenarios handling Activity on a post you are following on support.bioconductor.org User iranmdl15 wrote Question: customProDB: "complex" SNV scenarios handling: Hello all! I am about using customProDB for the first time and I have several questions regarding the package functionalities: 1) Does customProDB accept phased VCF file and produce accordingly the different protein products from each allele depending on the phase in the VCF file? 2) How does customProDB treat multiple variants affecting to a single amino acid (single codon)? Let's say that we have 2 non-synonymous variants at different positions of a given codon. Thank you in advance, Post tags: customprodb You may reply via email or visit customProDB: "complex" SNV scenarios handling
ADD COMMENT

Login before adding your answer.

Traffic: 228 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6