Gene variation study with number of genomes · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Gene variation study with number of genomes

I tired to find a gene variation with in 400 genome by flowing steps

bwa index 400genome.fasta

bwa mem 400genome.fasta gene.fasta >out.sam

samtools view -bt 400genome.fasta  out.sam >out.bam

samtools index out.bam

samtools mpileup -u -f 400genome.fasta out.bam>out.vcf

bcftools call  -m -v out.vcf >aa.txt

I did not get any variation form bcftool out. But when i tried with one genome as reference, bcftool shows some variation. Is there any problem in my steps?

gene genome snp bwa samtools

• 1,158 views • link

written 10.4 years ago by Eva_Maria

Hello akhilvbioinfo!

We believe that this post does not fit the main topic of this site.

I feel you just cant post the commands and ask whats wrong. You need to make sure the quality of data at every step and figure out whats happening by inspecting the outputs. You have not provided any details about what is 400 genome and what is one genome. What are you exactly looking at by aligning one gene etc.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link

written 10.4 years ago by GouthamAtla

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Problem generating a .vcf after upgrade of samtools and bcftools
written 3.4 years ago by Andy •

Hi I used to go over candidate sites of variation using SAMtools mpileup after which I used to execute some evaluations of the data using …
No variants found ( have problem in the handbook)
written 3.5 years ago by quanyu •

I am new in bioinformatics. Today I was studying variation calling fllowing "the biostars handbook", when I found a bug out of my knowledge. Here …
Left or right join between 2 BAM files (remove reads the should be filtered out for sex chromosomes)
written 3.7 years ago by beausoleilmo

I want to use this reference genome [Camarhynchus parvulus](https://www.ncbi.nlm.nih.gov/genome/84210?genome_assembly_id=838806) but it lacks information about the sex chromosomes (it only has Z chromosome, but not W). …
Mapping multiples
written 4.9 years ago by assane.mbodj •

Hi, I am coming to you for help. I am doing a mapping on short and long read files with BWA and MINIMAP2 My problem …
convert genome assembly to vcf file (Variant Call Format)
written 5.2 years ago by cabraham03 •

is any way to convert an assembly of a genome in contigs to vcf file (variant call format) ?? I have some genomes in fastq …
bcftools mpileup create an empty output file
written 5.8 years ago by Assa Yeroslaviz

I try to run `bcftools` to create a vcf file of my data, but I keep getting empty output files The command I use are …
non-SNP variants in a vcf merge file
written 6.8 years ago by evelyn

Hello, I have used `bwa` for alignment and `platypus` for variant calling and filtered only `SNPs` using `bcftools`. I then merged the vcf files with …
How to set up my vcf with a minimum depth?
written 7.1 years ago by apl00028

I am trying to set up the minimum depth which samtools mpileup considers a polymorphism for RNAseq samples. For that I did this: I did …
Weird issue with bam file generated by samtools
written 9.6 years ago by lakhujanivijay

I generated a bam file following the below steps: **indexed reference genome** bwa index reference.fasta **aligned using bwa mem** bwa mem ref.fasta f1.fq.gz f2.fq.gz > …
Empty VCF file with bcftools call
written 10.3 years ago by AP

Hello, I am trying to produce a vcf file using bcftools call but it produces an empty vcf file containing only the header. In short, …