Question: SNPhylo does not obey number of autosome chromosomes
0
gravatar for viniciushs.z
2.2 years ago by
viniciushs.z20
Brazil
viniciushs.z20 wrote:

I am trying to run the SNPhylo (http://chibba.pgml.uga.edu/snphylo/) but I am just unable to limit the number of chromosomes accordingly. In theory if I specify '-a' parameter it should limit the number of chromosomes. However, this apparently is not working.

~>snphylo.sh -d example.gds -a 12
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Hint: it is suggested to call `snpgdsOpen' to open a GDS file instead of `openfn.gds'.
SNP pruning based on LD:
Removing 19747 SNP(s) on non-autosomes
Removing 43508 SNPs (monomorphic: TRUE, < MAF: 0.1, or > missing rate: 0.1)
Working space: 128 samples, 71876 SNPs
        Using 1 (CPU) core
        Sliding window: 500000 basepairs, Inf SNPs
        |LD| threshold: 0.1
Chromosome 1: 4.33%, 692/15966
Chromosome 2: 4.34%, 460/10599
Chromosome 3: 3.88%, 345/8893
Chromosome 4: 3.41%, 299/8780
Chromosome 5: 3.24%, 220/6788
Chromosome 6: 2.95%, 148/5017
Chromosome 7: 3.03%, 137/4528
Chromosome 8: 2.80%, 117/4180
Chromosome 9: 2.16%, 104/4825
Chromosome 10: 2.47%, 101/4096
Chromosome 11: 2.51%, 85/3392
Chromosome 12: 2.04%, 94/4603
Chromosome 13: 1.75%, 89/5088
Chromosome 14: 1.58%, 80/5069
Chromosome 15: 1.93%, 68/3515
Chromosome 16: 4.03%, 5/124
Chromosome 17: 1.45%, 65/4498
Chromosome 18: 1.18%, 51/4304
Chromosome 19: 1.70%, 58/3415
Chromosome 20: 1.82%, 79/4351
Chromosome 21: 1.48%, 37/2503
Chromosome 22: 2.24%, 19/850
3353 SNPs are selected in total.

I would be grateful for any help here.

snphylo • 1.1k views
ADD COMMENTlink modified 8 months ago by nataliagru110 • written 2.2 years ago by viniciushs.z20
1
gravatar for arnstrm
2.2 years ago by
arnstrm1.7k
Ames, IA
arnstrm1.7k wrote:

Ah, found it! If you take a look at their script on GitHub, you'll see that they've hardcoded the number of chromosomes as 22!

num_last_autosome=22

(line 71) Just edit it to desired number of chromosomes and it should work fine!

ADD COMMENTlink written 2.2 years ago by arnstrm1.7k

Nevermind. In order to edit the template file in linux you use emacs.

emacs snphylo.template

Change the parameters as you see fit. then control x c to save the changes.

Then execute your snphylo pipeline.

Thank you.

ADD REPLYlink modified 8 months ago • written 8 months ago by nataliagru110
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