Checking for No-Calls

[jbarry6899]

Is there a program I can use on my Mac to check my BigY results for no-calls. I'm interested in finding out whether several specific SNPS, which dont appear on my list but do on my closest matches, were no-calls in my test.

Jim

[dtvmcdonald]

Odd that no replies have appeared.

Answer is yes. Excel or any text editor will do.

You need to download the vcf and bed files. These are
text files.

You need the exact location of the SNP. Since you
are comparing, you should have those.

Look at the VCF file first. If it has the location,
that is your answer.

If not, look at the bed. This is trickier.

It has things like:
chrY 2725567 2725575
chrY 2725576 2725585
chrY 2725685 2728126
chrY 2728127 2728129
chrY 2728130 2728167
chrY 2728187 2729628

This means that the computer has made calls
in the regions:

2725568 2725575
2725577 2725585
2725686 2728126
2728128 2728129
2728131 2728167
2728188 2729628

notice the difference in the first column! You
add one to that column to get the areas where there are reads! I.e.

2725576 and
2728126 and
2728130 are single no-calls, and there are
also some large areas of nocalls.

If its not in the vcf file and IS listed as a call in the bed, its the reference allele.

But this is NOT definitive. Definitive is MUCH harder!
First you get the BAM file from FTDNA .
Then you need to download a program call IGV
http://www.broadinstitute.org/software/igv/download
and learn to use it. Load up your bam file in IGV. You look up a location
in the viewer and look at the raw data ... you may decide
that FTDNA's "caller" program was too conservative.
Actually once you figure out how to use IGV its very very easy. You really should load up several bams at once and
compare the same location in them.

I have looked at dozens of markers in dozens of bam files
and many questions can be answered reliably by
suspecting a location is either + or - because of
the suspected phylogeny and looking in the bam.

Yes, needing to use the bams is a real drag.

[JimKane]

If its not in the vcf file and IS listed as a call in the bed, its the reference allele..

This statement should be qualified with "usually" it's the reference. There are times when you open up the BAM, you'll find there are between 1 and 3 derived reads when the ancestral seems inconsistent with a kit's matches.

Ultimately, if you want to check no calls you have go to the BAMs as you mentioned.