My VCF files are of zero length?
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?
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mahnoornaseer97 •
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what are the errors messages ? why do you post this post with the 'R' tag ?
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:
i have edited my question. there are no error message its just that the vcf files does not have any information after the header?