hi all
I am trying to create a mpileup file so I can get vcf file which I can run on IGV and can use for SNP calling
but i am facing following problems:
i gave following command for mpile up file:
source samtools
samtools mpileup -E -uf reference.fa file.sorted.bam > file.mpileup
it gave output:
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
and computer stucks here
when i restart, a mpileup is created
then i try to creat vcf file from that mpileup by giving following command:
source bcftools
bcftools view -cg file.mpileup > file.vcf
error occurs:
Error: Could not parse --min-ac g
can anyone help me in that i am stuck at SNP calling
I am trying to create a mpileup file so I can get vcf file which I can run on IGV and can use for SNP calling
but i am facing following problems:
i gave following command for mpile up file:
source samtools
samtools mpileup -E -uf reference.fa file.sorted.bam > file.mpileup
it gave output:
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
and computer stucks here
when i restart, a mpileup is created
then i try to creat vcf file from that mpileup by giving following command:
source bcftools
bcftools view -cg file.mpileup > file.vcf
error occurs:
Error: Could not parse --min-ac g
can anyone help me in that i am stuck at SNP calling
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