what is vcf fie ? it is mean?

Question

[yousefifariba6]

Min coverage:   8
Min reads2: 2
Min var freq:   0.01
Min avg qual:   15
P-value thresh: 0.99
Reading input from STDIN
20648 bases in pileup file
1425 variant positions (1392 SNP, 33 indel)
272 were failed by the strand-filter
1425 variant positions reported (1392 SNP, 33 indel)

what is mean?

[Kevin Blighe]

Hello yousefifariba6. Welcome. Please, you can show the code that you used to generate this output?

Please note that:

• 'Min' == 'Minimum'
• 'var freq' == 'variant frequency'
• 'avg' == 'average'

What is the aim of your experiment? Thank you!

Answer 1

[jared.andrews07]

Wikipedia actually does a decent job explaining the VCF format, though you can always look at the actual specifications as well. Pay close attention to the version of your file, as the spec has been changed slightly over time.

As for what the stats in your post mean, we need way more info about what you're running to answer that in any meaningful way.