Using the IGV for vcf files, quality scores

[jrhyno]

When I'm looking at genotypes in the IGV (vcf files), there is a quality score. What does this mean, and is there a number below which I shouldn't have any confidence in the number?

I've tried to find a good answer, but haven't so far.

Thanks,

Jeff

[ajhalawani]

Hi Jeff,

IGV is a tool for visualisation using BAM and BAI files to check your sequencing. You can look at the quality when you point to the read and the number of the quality is based on Phred score. For example a read of quality 20 means that the probability of that base to be incorrect is 1 in 100 and that gives an accuracy of 99%. Any number above the 20 means you get a higher quality of that based called. 20 is the standard as was set during the Human Genome Project.

I hope this help.

[GenomExpert]

Dear all
i have two problems:
1. i am a new user so would u people help me please to how to interpret the IGV output.
2. since the very begining am facing a problem when i use mpileup to convert my BAM to BCF, it generate error like;
[mpileup] 1 sample in one input file
<mpileup> set max per-file depth to 8000
[bcf_sync] incorrect number of fields (0 !=5) at 0:0
[afs] 0:0.000
please it has already wasted my enough time so help me out of this error.

[dpryan]

Firstly, please start a new thread.

Secondly, that error typically happens when there's a mismatch between your samtools and bcftools versions. Ensure you have the most recent release of both. Also, post the exact command you used that produced the error.