Questions tagged [bcftools]
The bcftools tag has no usage guidance.
30
questions
4
votes
1
answer
64
views
Can not launch bcftools using python's subprocess module, as it only accepts first command of commands list
I am trying to remove samples from a chromosome vcf file. I wrote a function that takes chromosome number and a list of samples to remove. When I try to run bcftools using subprocess module it only ...
- 171
2
votes
0
answers
30
views
bcftool merge of 5K samples makes ID a large string
I am using bcftools to merge 5000+ vcf files using this command
bcftools merge -l list_of_vcfs.txt
I am getting the following error
...
- 21
2
votes
2
answers
118
views
How can I retrieve the GRCh38 coordinates of a list of rsids?
I have a list of about 100,000 rsids and I want to get their genomic coordinates on the GRCh38 genome build. Is there a command line tool that allows me to do this? If yes, which one?
I have tried ...
- 105
3
votes
3
answers
1k
views
Strategy for merging many VCFs
Can anyone suggest a strategy for speeding up VCF merging?
I have ~44,000 single-sample VCFs that I am trying to merge into a multi-sample VCF with bcftools merge, ...
- 663
3
votes
2
answers
170
views
Non-ACGTN alternate alleles in VCF
I was trying to left normalize my vcf file using following command:
bcftools norm -f reference.fasta -m -any input.vcf > output.norm.vcf
However this gives the ...
- 160
1
vote
1
answer
134
views
Bcftools 1.16 able to add F_MISSING tag?
I tried adding the F_MISSING tag using bcftools 1.16. When I run this command:
...
- 11
1
vote
2
answers
322
views
Large amount of REF prefix differences after lifting
I lifted some unmerged trio files from hg19 to hg38 using liftOverPlink. It looks like that several houndred allels on each chromosome of one file shifted/switched to non-standard alleles. I recorded ...
- 145
3
votes
1
answer
329
views
Filter with bcftools
I want to filter a SNP, specifically CHROM1:POS:630128. I tried to use bcftools for this.
I came up with the following variant ...
- 145
2
votes
1
answer
60
views
Can I discard missing alleles?
I am converting a biallelic VCF into a SQL table and one of my tables will be something like:
...
- 123
2
votes
0
answers
97
views
BAF and LRR calculation and usage
I'm working with a vcf file, in particular I'm trying to identify a gene duplication in a sequenced genome.
I studied bcftools cnv command, but for this tool is needed a vcf file containing a BAF and ...
- 21
2
votes
1
answer
575
views
Compare VCF files
I have two strains, X and Y, and I would like to compare the variants found in both. I have my own parent strain, Z, that was sequenced and assembled to be used as the reference genome.
I first ...
- 804
4
votes
0
answers
129
views
Error occurrence after merging files with bcftools: wrong number of fields?
This question was also asked on Biostars
I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff and SnpSift.
First pair vcf -> only variations| CASES and CONTROLS
Second ...
- 141
1
vote
1
answer
373
views
bcftools mpileup "Failed to open the file" questions
When I trying to use bcftools mpileup to convert bam to vcf files,
I try to use:
...
- 135
0
votes
1
answer
717
views
Filtering a vcf with a text file of SNP rsIDs
I have a vcf file containing an ID field with a snps and a list of human SNPs from dbSNP.I want to remove whatever in dbSNP from vcf file. The text file is like this:
...
- 1,951
0
votes
0
answers
56
views
Combine all alternate alleles
I have a vcf with multi-allelic SNPs, e.g. REF: A and ALT: G, C.
I would like to combine all reference alleles to the most ...
- 101
0
votes
1
answer
163
views
Convert VCF file to mpileup.txt
I am working on an iterative analysis that uses orthologous pipelines that require mpileup.txt files as input for a visualization step. This requires me to convert VCF files to mpileup.txt.
This ...
1
vote
2
answers
518
views
How do I call variants using BCFTools without piping mpileup file?
I need to call variants on a large number of reads using both VarScan2 and BCFTools. Both of these variant calling tools use <...
- 133
0
votes
1
answer
84
views
Snakemake rule issue with bcftools view filtering
I am creating a bioinformatics pipeline using Snakemake doing everying from adapter trimming of raw sequencing data in .fq to mapping, SNP calling and SNP filtering.
The issue i am having is when i ...
- 85
2
votes
0
answers
501
views
What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?
This question was also asked on Biostars
Consider this minimal VCF file which contains a multi-allelic call made by a somatic variant caller on a human tumor sample:
...
- 9,452
1
vote
3
answers
748
views
Masking sites in a vcf file
I need to mask all sites in a vcf file flagged by the 1000 Genomes Project as being unfit for population genetic analyses. The sites for all chromosomes are available at:
1000Genomes masked sites
From ...
- 115
0
votes
0
answers
1k
views
Filtering samples by FORMAT attributes using bcftools
The -e and -i options of the bcftools filter command appear, by default, to only allow for ...
- 101
2
votes
1
answer
2k
views
How to generate a consensus sequence from a multi-reference BAM file?
I am trying to generate a consensus sequence from a BAM file that was generated by mapping reads to a reference FASTA containing multiple sequences.
Usually, I generate consensus sequences from BAM ...
1
vote
0
answers
266
views
How to filter allele frequency VEP with bcftools?
I have a VEP annotated VCF file, and I wish to use bcftools to filter it. bcftools work very well on standard VCF fields, but I'm not able to make it work on VEP fields.
For example, the following ...
- 2,739
2
votes
0
answers
270
views
Subsetting SNPs with specific exclusion criteria using bcftools
I am trying to subset SNPs from 32 cultivars. I have the following exclusion criteria:
>20% missing data
SNPs present in less than 50% of genotypes
Each genotype must have at least 50% of included ...
- 21
1
vote
0
answers
711
views
Create a genotype matrix from VCF file using bcftools
I have a vcf file that contains SNPs from chromosome 2 for 2000 samples. I want to create a genotype matrix from this vcf file.
The file is in zipped format as well so that I can use ...
- 341
0
votes
2
answers
675
views
Generate VCF from different .bam files with different chromosome names
I have two resources of .bam files. One is generated by our lab (1 sample = 1 bam). One is downloaded online (again 1 sample = 1 bam). For the downloaded samples the chromosomes are labelled: chr1, ...
- 101
1
vote
1
answer
70
views
How to do the reverse of bcf merge?
How can one do the reverse of bcftools merge?
To get one sample back out of the merged one.
Without holding reference sites.
2
votes
2
answers
645
views
extracting last few lines of a growing bgzip compressed .vcf.gz file
I am running bcftools merge to create a single .vcf.gz file out of a collection of chromosomal ...
- 2,294
5
votes
3
answers
4k
views
How to get fasta alignment file from SAM/BAM file?
I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's ...
- 357
5
votes
3
answers
609
views
bcftools filtering all files in a directory
Probably a silly oversight on my part, but I'm trying to filter all the vcfs in a directory with bcftools using a simple loop. My basic command is working fine:
...
- 305