SNPhylo does not obey number of autosome chromosomes

Question

[viniciushs.z]

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.

Answer 1

[arnstrm]

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!

[nataliagru1]

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.