Question: My VCF files are of zero length?
0
gravatar for mahnoornaseer97
14 months ago by
mahnoornaseer970 wrote:

i have sorted bam files , i used these command to generate VCF file but my file only has headers, it does not show any alignment?

this is the code that i used

> samtools mpileup -u -f /home/mahnoor/--------------/reference.fa      /home/mahnoor/Documents/IGV_DATA/Wheat_DATA/REFERENCE.sorted > /home/mahnoo---------------/SRR030257.bcf
------- to generate bcf file

> bcftools view -v -c -g /home/mah-------Documents/IGV_DATA/Wheat_DATA/SRR030257.bcf > /home/mahn -------/Documents/IGV_DATA/Wheat_DATA/test_wheat/test_data/SRR030252.vcf
--------to generate vcf file



    #CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT   ------ there is nothing after this?

///////// there is no error its just that when i generate the vcf file it does not have any information after the lines above?

next-gen alignment • 459 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by mahnoornaseer970

what are the errors messages ? why do you post this post with the 'R' tag ?

ADD REPLYlink written 14 months ago by Pierre Lindenbaum112k

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

ADD REPLYlink written 14 months ago by WouterDeCoster32k

i have edited my question. there are no error message its just that the vcf files does not have any information after the header?

ADD REPLYlink written 14 months ago by mahnoornaseer970
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