Stack Depth for each locus in outputs?

joshua....@gmail.com

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Apr 22, 2015, 5:21:07 PM4/22/15

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Hi there,

I tried searching through the wealth of knowledge in this google group, but I think that by definition my search terms are too vague, making it impossible to find a relevant question/answer. I'm simply trying to find the stack depth for each locus in a format on which I can run some basic summary statistics. I know that I can look at each individual locus in the php viewer and see the stack depth, but I'm interested to know the min, max, mean and median values or plot a histogram of stack depths for all twenty-some thousand SNPs that I've got. I set -m 3 in denovo_map.pl, and now I'd like to see what the true distribution of stack depths turned out to be compared to the minimum requirement.

Any insight as to where this information can be found would be much appreciated. I've looked through the output files but don't see any fields that appear to represent stack depth, and again I wasn't able to narrow down my search much in these forums due to the vagueness of search terms such as 'stack depth locus', so I gave up after reading a few dozen threads without success :-)

Thanks!

Cheers,

Josh

Julian Catchen

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Apr 22, 2015, 5:29:28 PM4/22/15

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Hi Josh,

The ustacks/pstacks programs output the average pre- and post-merge
stack depths. If you ran them via denovo_map.pl or ref_map.pl they will
have been captured in denovo_map.log or ref_map.log files.

You can find total locus depth and individual allele depths for each SNP
output in the VCF file.

You can also get allele depths output using the export_sql.pl file,
which will export them from the database.

The raw allele depths are in the *.matches.tsv files.

Best,

julian