bam2mpg output

[m_elena_bioinfo]

Dear all,
I'm trying BAM2MPG software to analyze the goodness of my variant call.
But I can't understand the output when i run
> bam2mpg hg19.fasta sample.bam

This is the output:
MPG_SNV chr1 824017 g AA 0 1 1
MPG_SNV chr1 835499 A GG 0 1 1
MPG_SNV chr1 846489 T CC 0 1 1
MPG_SNV chr1 852758 G CC 0 1 1
MPG_SNV chr1 862093 T CC 0 1 1
MPG_SNV chr1 862124 A GG 0 1 1
MPG_SNV chr1 862383 C TT 0 1 1
MPG_SNV chr1 862389 A GG 0 1 1
MPG_SNV chr1 865219 G AA 0 1 1
MPG_SNV chr1 869303 C TT 0 1 1
MPG_SNV chr1 869323 T CC 0 1 1
MPG_SNV chr1 869369 G TT 0 1 1
MPG_SNV chr1 869373 G CC 0 1 1
MPG_SNV chr1 869401 G CC 0 1 1
MPG_SNV chr1 879563 A GG 0 1 1
MPG_SNV chr1 895706 G AA 0 1 1

Anyone could explain me what are the values in last three columns?
Thankx a lot
ME

[nhansen]

Hi ME--

The final three columns are:

genotype score: a reasonable cutoff for a high quality genotype is 10, corresponding to expected accuracy of roughly 99.9%.

ref/nonref column: this column is one when the genotype contains an allele that doesn't match the reference (useful for pulling variants with "awk").

coverage: the number of reads used to call the genotype (if you are using the --qual_filter option, low quality reads won't be counted).

It looks from your output like you have only one read in this region, and that the bases don't match the reference. My best guess is that you're specifying the wrong reference fasta file. What does this region look like if you view it in samtools tview or IGV?

--Nancy

[m_elena_bioinfo]

Thank you Nancy, you are right! I was using the wrong reference fasta file. Now bam2mpg run correctly and your explanation about the column data are very useful for me!

[nhansen]

Great! I'm sorry I didn't notice your post earlier--glad you're getting good use of the program. There's actually fairly extensive documentation within the perl script, so type "perldoc bam2mpg" to get more information on options and output.

--Nancy