Question: How to generate vcf using samtools Version: 0.1.19-96b5f2294a?
0
gravatar for Vijay Lakhujani
3.2 years ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

I am new to NGS and I am stuck at a point where I need to generate .vcf file using a BAM file and a genome. I am on Ubuntu 14.0. I have samtools v0.1.19-96b5f2294a

Here is the output when I type in 'samtools mpileup' and hit enter

samtools mpileup

Usage: samtools mpileup [options] in1.bam [in2.bam [...]]

Input options:

       -6           assume the quality is in the Illumina-1.3+ encoding
       -A           count anomalous read pairs
       -B           disable BAQ computation
       -b FILE      list of input BAM filenames, one per line [null]
       -C INT       parameter for adjusting mapQ; 0 to disable [0]
       -d INT       max per-BAM depth to avoid excessive memory usage [250]
       -E           recalculate extended BAQ on the fly thus ignoring existing BQs
       -f FILE      faidx indexed reference sequence file [null]
       -G FILE      exclude read groups listed in FILE [null]
       -l FILE      list of positions (chr pos) or regions (BED) [null]
       -M INT       cap mapping quality at INT [60]
       -r STR       region in which pileup is generated [null]
       -R           ignore RG tags
       -q INT       skip alignments with mapQ smaller than INT [0]
       -Q INT       skip bases with baseQ/BAQ smaller than INT [13]
       --rf INT     required flags: skip reads with mask bits unset []
       --ff INT     filter flags: skip reads with mask bits set []

Output options:

       -D           output per-sample DP in BCF (require -g/-u)
       -g           generate BCF output (genotype likelihoods)
       -O           output base positions on reads (disabled by -g/-u)
       -s           output mapping quality (disabled by -g/-u)
       -S           output per-sample strand bias P-value in BCF (require -g/-u)
       -u           generate uncompress BCF output

SNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):

       -e INT       Phred-scaled gap extension seq error probability [20]
       -F FLOAT     minimum fraction of gapped reads for candidates [0.002]
       -h INT       coefficient for homopolymer errors [100]
       -I           do not perform indel calling
       -L INT       max per-sample depth for INDEL calling [250]
       -m INT       minimum gapped reads for indel candidates [1]
       -o INT       Phred-scaled gap open sequencing error probability [40]
       -p           apply -m and -F per-sample to increase sensitivity
       -P STR       comma separated list of platforms for indels [all]

Notes: Assuming diploid individuals.

 

I am giving following command:

samtools mpileup –f wu_0.v7.fas –uv out.full.sorted.bam > out.full.mpileup.vcf

I get below error:

mpileup: invalid option -- 'v'
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

 

Please help

samtools ubuntu vcf • 1.5k views
ADD COMMENTlink modified 3.2 years ago by Devon Ryan89k • written 3.2 years ago by Vijay Lakhujani4.0k
0
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

As you can see, there is no "-v" option in that version. You need to pipe the bcf file to bcftools.

ADD COMMENTlink written 3.2 years ago by Devon Ryan89k

Thanks Devon,

But sorry I am very naive user. Can you help me with the command set?

here are some details:

genome -  wu_0.v7.fas

BAM file  - out.full.sorted.bam (i sorted it using samtools)

 

Please help

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Vijay Lakhujani4.0k

Read the output of "bcftools view". Note that I really can't recommend using such outdated versions of samtools and bcftools through.

ADD REPLYlink written 3.2 years ago by Devon Ryan89k
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