Question: How to convert vcf to MAF ?
0
gravatar for sunnykevin97
13 months ago by
sunnykevin9730
sunnykevin9730 wrote:

I'm interested in converting vcf to MAF, I found 2 scripts

1) perl vcf to maf

Its ask for a EXAC vcf for filtering,

2) Python vcf to maf (https://github.com/cbare/vcf2maf)

python vcf2maf.py --vcf  /data/genome/RG.vcf --maf testmaf -o permaf
**"Traceback (most recent call last):
  File "vcf2maf.py", line 556, in <module>
    main()
  File "vcf2maf.py", line 543, in main
    n += vcf2maf(vcf_file, maf_file, decrement_end_coordinate=args.decrement_end_coordinate, verbose=args.verbose)
  File "vcf2maf.py", line 184, in vcf2maf
    centers = vcf_reader.metadata['center']
KeyError: 'center**'

I'm facing error

or is their any alternatives to convert vcf to MAF?

Thanks!

snp alignment • 1.2k views
ADD COMMENTlink modified 13 months ago • written 13 months ago by sunnykevin9730

Hi

I setup the paths in .bashrc, still not able run ?

# VEP #
export PATH="/usr/local/softw/ensembl-vep:$PATH"
export PATH="/mnt/NAS/projects/VEP/loxodonta_africana:$PATH"

I edited the path in VCF2MAF.pl

my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele ) = ( "/usr/local/softw/ensembl-vep", "/mnt/NAS/projects/VEP/loxodonta_africana", 4, 5000, 0 )

Were it went wrong ?

thanks!

ADD REPLYlink modified 13 months ago by genomax76k • written 13 months ago by sunnykevin9730

post the error message you're getting if it's still not working

ADD REPLYlink written 13 months ago by Barry Digby250

HI

./vcf2maf.pl --input-vcf /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vcf --output-maf /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005.maf --species loxodonta_africana --filter-vcf 0  --ref-fasta /mnt/NAS/projects/2018/ref/LoxArf4.fasta --vep-path /usr/local/softw/ensembl-vep --vep-data /mnt/NAS/projects/2018/VEP/loxodonta_africana/ 
STATUS: Running VEP and writing to: /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vep.vcf

-------------------- EXCEPTION --------------------
MSG: ERROR: Cache directory /mnt/NAS/projects/2018/VEP/loxodonta_africana//loxodonta_africana not found

STACK Bio::EnsEMBL::VEP::CacheDir::dir /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311
STACK Bio::EnsEMBL::VEP::CacheDir::init /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
STACK Bio::EnsEMBL::VEP::CacheDir::new /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /usr/local/softw/ensembl-vep/vep:224
Date (localtime)    = Mon Dec 24 20:54:22 2018
Ensembl API version = 94
---------------------------------------------------

ERROR: Failed to run the VEP annotator! Command: /usr/bin/perl /usr/local/softw/ensembl-vep/vep --species loxodonta_africana --assembly GRCh37 --offline --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /mnt/NAS/projects/2018/VEP/loxodonta_africana/ --fasta /mnt/NAS/projects/2018/ref/LoxArf4.fasta --format vcf --input_file /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vcf --output_file /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vep.vcf --fork 4 --regulatory
ADD REPLYlink modified 13 months ago by genomax76k • written 13 months ago by sunnykevin9730

sunnykevin97 : Please use ADD REPLY when responding to existing comments to keep threads logically organized.

ADD REPLYlink written 13 months ago by genomax76k
1
gravatar for Raony Guimarães
13 months ago by
Dublin / Ireland
Raony Guimarães1.1k wrote:

Perl method works well and is the most recommend :)

https://github.com/mskcc/vcf2maf

You don't necessarily need an EXaC vcf to annotate, but you will need VEP.

ADD COMMENTlink written 13 months ago by Raony Guimarães1.1k

I tried facing an error ..

Is their 2 formats - 1) multiple alignment format 2) mutation annotation format I'm interested in converting vcf to multiple alignment format is their any tool ?

ADD REPLYlink written 13 months ago by sunnykevin9730

I'm currently working with elephants datasets

ADD REPLYlink modified 13 months ago • written 13 months ago by sunnykevin9730

It is not possible to convert VCF format to multiple alignment format because one represents variants and the other represents sequence alignments. VCFs can be converted to mutation annotation format because both represent variants.

ADD REPLYlink written 10 months ago by Cyriac Kandoth5.4k
1
gravatar for Barry Digby
13 months ago by
Barry Digby250
National University of Ireland, Galway
Barry Digby250 wrote:

When using vcf2maf.pl you have to edit the paths of files in the script. Following up with what Raony Guimarães said, you will need VEP, and you will also need to specify its path:

nano vcf2maf.pl :

# Set any default paths and constants
...
my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele ) = ( "$ENV{HOME}/vep", "$ENV{HOME}/.vep", 4, 5000, 0 );

Set "$ENV{HOME}/vep" to your path containing "node00/example/VEP/ensembl-vep"

Set "$ENV{HOME}/.vep" to your path containing your genome builds, snp sites etc. "node00/example/VEP"

my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/91_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz", "$ENV{HOME}/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz" );

Again change instances of '$ENV{HOME}/.vep" to path containing genome builds etc

ADD COMMENTlink modified 13 months ago • written 13 months ago by Barry Digby250

HI, this was the error I'm facing ?

./vcf2maf.pl --input-vcf /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vcf --output-maf /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005.maf --species loxodonta_africana --filter-vcf 0  --ref-fasta /mnt/NAS/projects/2018/ref/LoxArf4.fasta --vep-path /usr/local/softw/ensembl-vep --vep-data /mnt/NAS/projects/2018/VEP/loxodonta_africana/ 
STATUS: Running VEP and writing to: /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vep.vcf

-------------------- EXCEPTION --------------------
MSG: ERROR: Cache directory /mnt/NAS/projects/2018/VEP/loxodonta_africana//loxodonta_africana not found

STACK Bio::EnsEMBL::VEP::CacheDir::dir /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:311
STACK Bio::EnsEMBL::VEP::CacheDir::init /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
STACK Bio::EnsEMBL::VEP::CacheDir::new /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
STACK Bio::EnsEMBL::VEP::Runner::init /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /usr/local/softw/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /usr/local/softw/ensembl-vep/vep:224
Date (localtime)    = Mon Dec 24 20:54:22 2018
Ensembl API version = 94
---------------------------------------------------

ERROR: Failed to run the VEP annotator! Command: /usr/bin/perl /usr/local/softw/ensembl-vep/vep --species loxodonta_africana --assembly GRCh37 --offline --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /mnt/NAS/projects/2018/VEP/loxodonta_africana/ --fasta /mnt/NAS/projects/2018/ref/LoxArf4.fasta --format vcf --input_file /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vcf --output_file /mnt/NAS/projects/2018/M.perminguis/PERMINGIUS_G-2005_915_merged_rmdup_RG.bam_GATK.vep.vcf --fork 4 --regulatory
ADD REPLYlink written 13 months ago by sunnykevin9730

Do not edit code to change the values of $vep_path and $vep_data. Use command-line arguments --vep-path and --vep-data instead. Please see more in documentation printed when using argument --help.

ADD REPLYlink written 10 months ago by Cyriac Kandoth5.4k
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