Good morning, everyone!
I am using bcftools for genome assembly and extracting consensus sequences of viral genomes. Firstly, I noticed that...
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bcftools genome assembly doubt
Last edited by felipe.iani; 05-20-2024, 05:48 AM. -
Insertions follow reference in vcf file
Hi,
I'm working with gvcf files, containing also non-variant positions. I have noticed some insertions that I'm not able to correctly interpret... -
Bcftools installed via Cygwin plugin error
Hi! I am trying to look at several genomes of different individuals of the same species and call the SNPs for each genome using bcftools. I installed... -
R, vcfr, extrcat.gt, bcftools filter
Hello,
I have been unable to extract depth 'DP' info from my vcf files (generated with latest bcftools variant calling (SNPs)) after being converted...Last edited by wbsimey; 08-19-2021, 09:11 AM. -
Bcftools Mpileup bias for alternative alleles?
I have called snps from a bam file using the below commands:
...Code:/usr/local/sw/bcftools-1.9/bcftools mpileup -f /mnt/NEOGENE2/share/ref/genomes/hsa/hs37d5.fa
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How to get the information of GT (genotype) field in vcf files
Hi all,
I am new to SAMtools and bcftools
. I used Hisat2 for alignment, samtools for sorting and indexing and SNP calling. Here are...
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bcftools call: why is this a 1/1?
I can't for the life of me figure out why bcftools call genotypes this position (and many, many others like it) as 1/1:
Here's the input... -
vcftools and bcftools disagree
Hello,
I'm trying to impute my data using HRC (sanger server). For that I validated and annotated my vcf using GATK and then prepared... -
bcftools output type not recognized
I am trying to find a single SNP on a bunch of dog genomes in a compressed vcf file (vcf.gz) and I have been using bcftools to do so. I posted before... -
SNP calling using samtools
Hi all,
I have RNA-seq paired-end data from Illumina and I am using BWA-mem for mapping and samtools for SNP calling. I wanted to understand... -
bcftools - retain low quality read position support?
Is it possible to have `bcftools call -c` output a DP4 values that add up to the total DP value. I want to call simple consensus sequences based on a... -
bcftools is slow
Hi,
I am subsetting a vcf by positions stored in a tab delimited file using bcftools. I noticed the program is very slow. Here is the command:... -
some variants disappear after bcftools norm
Hello,
I noticed that when performing left-normalization on my vcf file (as suggested by Annovar at http://annovar.openbioinformatics.... -
add missing annotations to vcf
I am using bcftools version 1.3.1 and trying to add undefined annotations to a vcf before using bgzip and tabix.
If I try to run the norm...Last edited by cmccabe; 03-01-2017, 04:55 AM. -
Question: bcftools: Wrong number of PL fields? nals=4 npl=6
Hello all,
I am new to bcftools and samtools, so forgive my question if it is ignorant. My goal is to extract consensus sequences between...
