Comments (4)
Hi @Salvobioinfo -- sorry to hear that faToVcf isn't working as you expect. faToVcf uses the first sequence in the input fasta file as reference, unless you add the -ref=seqName option (where seqName is the name of the reference sequence, which must be included in the input fasta file). In order to help us diagnose, I have a few questions:
- How did you install faToVcf? bioconda? Download executable? Build from source? When did you last install or update it?
- What is the exact faToVcf command that you ran? (It will help to see the exact options used)
- Better yet, if you can run the same faToVcf command but add
-verbose=2
, and then copy-paste both the command and the stderr messages from the terminal into a reply, that will provide additional clues. - Best of all, if you can share the fasta input then I can try to run the same command -- but I understand that it's not always possible to share.
from kent.
Thanks @Salvobioinfo -- it helps to know that you're using the GISAID MSA. That file uses a masking character that faToVcf does not expect: it uses '-' instead of 'N' to mask sites that are known to be problematic when building phylogenetic trees. When faToVcf sees a '-', it interprets that as an alignment gap not an N or masked base. When it sees '-' in the reference sequence, it assumes that some other sequence has an insertion at that location, and it skips over that base in all input sequences. However, if '-' is used as a masking character not an alignment gap, then faToVcf's assumption is incorrect and it results in incorrect coordinates in the output.
Here's how to work around that.
- Make a fasta file with only unmasked EPI_ISL_402124 sequence (not extracted from the MSA file -- the original sequence from GISAID), say
EPI_ISL_402124.fa
. - Edit
EPI_ISL_402124.fa
to make sure that the sequence name after>
is not exactly "EPI_ISL_402124". (The long hCoV-19/.... name is fine, or only "WIV04" -- just not "EPI_ISL_402124".) - Don't use -includeRef and -ref; instead, concatenate
EPI_ISL_402124.fa
with2021-11-09_masked.fa
like this:
/dir/faToVcf -vcfChrom=NC_045512.2 -noGenotypes -ambiguousToN -verbose=2 \
<(cat EPI_ISL_402124.fa 2021-11-09_masked.fa) \
21-11-09_masked_EPI_ISL_402124.vcf > fatovcf_NC_045512.2.log 2>&1 &
EPI_ISL_402124 will still be included in the VCF because it is in 2021-11-09_masked.fa
, but the directly downloaded, unmasked sequence of EPI_ISL_402124 will be used as the reference, resulting in a masking behavior instead of gap-skipping behavior.
Hope that helps, and please let us know if any of that is unclear or if it doesn't work.
from kent.
Hi @AngieHinrichs,
1.Question:
I downloaded the executable following the instruction at this UCSC_link, the 13.11.2021.
2-3. Question:
The command I used is:
/dir/faToVcf -includeRef -ref=EPI_ISL_402124 -vcfChrom=NC_045512.2 -noGenotypes -ambiguousToN -verbose=2 2021-11-09_masked.fa 21-11-09_masked_EPI_ISL_402124.vcf > fatovcf_NC_045512.2.log 2>&1 &
The log file is:
fatovcf.log
4. Question:
I cannot share the file, but itβs possible to get it from GISAID. Itβs the MSA (masked).
Thank you in advance.
Best,
Salvo
from kent.
Dear @AngieHinrichs.
The tool works well now.
Thank you.
Salvo
from kent.
Related Issues (20)
- path issue for doBlastzChainNet.pl HOT 2
- Certificate validation (https.c) causing issues with build in v424 HOT 9
- profile db not found in sqlProfileToMyCnf()
- bedGraphToBigWig: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory HOT 1
- twoBitToFa: Can only handle version 0 of this file. This is version 1 HOT 1
- module in src/hg can't make with MySQL 8^ HOT 1
- `Response is missing required header Content-Length: for url ` HOT 11
- Bioconda package for kent HOT 4
- wigToBigWig doesn't work for chromosomes with spaces in name. HOT 3
- src/lib/htmshell.c doesn't compile on aarch64 Ubuntu 20.04 HOT 2
- Where can I download the pslSplitOnTarget binary? HOT 2
- Provide Linux aarch64 binary for genePredToGtf HOT 17
- Incorrect number of bytes for empty slots in rWriteLeaves HOT 5
- Proposal to remove S:417/440/505 in branch specific mask list.
- Bash reporting error HOT 1
- undefined reference to sqlSetIsUcscMirror HOT 1
- undefined reference HOT 2
- Question about classNet HOT 9
- errors reported by axtchain HOT 2
- undefined reference to `knet_init_alt'
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from kent.