Whitelist of single SNPs

[Shannon Kjeldsen]

Hi All,

I was wondering if there is a trick to gettting the populations module to write only selected single SNPs. I have Black and Whitelisted markers before (eg. ones which ave been identified as sex-linked or of non-target origin) with no issues, but if I try to create a whitelist with specific SNPs, I run into trouble and get a "Unable to load any markers from 'single_snp_whitelist.tsv'" error.

My working lists are .tsv files and look like this:

6

10

13

20

21

24

25

26

36

38

43

46

47

51

60

67

69

78

79

80

88

...

18490

and my whitelists that do not work look like this: 

6 47

10 160

13 86

20 150

21 106

24 57

25 156

26 81

36 110

38 12

43 191

46 27

47 184

51 108

60 27

67 172

69 167

78 108

79 64

...

18490 48

so the locus ID and SNP position separated by a tab (I have also tried replacing with spaces, with and without a return at the beginning and end of the files to no avail).

I'm sure I'm doing something very basic wrong, but any advice would be greatly appreciated.

Cheers,

Shannon 

[Julian Catchen]

Hi Shannon,

What version of Stacks are you using and how did you generate the SNP
positions in the second column? Are your reads longer than 150bp?

Best,

julian

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[Shannon Kjeldsen]

Hi Julian,

We are currently using STACKs v1.20 (been meaning to update it, but there has been a bit of a backlog of jobs on our server and the IT guys should get to it eventually)

I generated the list manually by producing a  structure output, I then filtered through the SNPs in excel to pick which subset I wanted (not the most efficient way, I know, but I wanted to play around with the data a bit), and each SNP is displayed as "6_47" etc in the structure file - so I'm assuming this is "SNP-ID_SNP-position" yes? 

I then picked out a specific list of SNPs I wanted to write to another structure file and just replaced the _ with a tab... Is there a better way to generate the list?

We have concatenated our F and R reads so that the reads are now 195bp long, is the length likely to be a problem? 

Cheers,

Shannon

 

[Julian Catchen]

Hi Shannon,

Unfortunately, the single-SNP whitelist was added in Stacks 1.21. Ping
me again if you have difficulty once you have upgraded.

Best,

julian

Shannon Kjeldsen wrote:

[Elizabeth Solorzano]

Hi all,

   I have a similar problem that Shannon with my whitelist, but the error that I obtained is : "unable to parse whitelist at line 1" My stacks version is 1.34 and my whitelist is a .tsv file, It has a tab space between loci and snp positición,  I have generated the list manually by producing a  genepop output, and look like this:

5 47

6 53

75 6

143 50

143 53

152 72

217 5

217 57

223 38

312 11

Best regards

[Nicolas Rochette]

This was solved, it was a carriage return issue. You can check your files with :

hexdump -C -n100 file.txt

(0A is a new line, 09 a tab, 0D a carriage return)

Nicolas

Norah Saarman wrote on 06/23/2016 12:52 PM:

Hi Julian,

I am having the same problem as Elizabeth and Shannon, with version 1.34.

My list looks like this:

232758 66

164737 61

207793 19

305653 26

7501 26

257921 15

109049 65

143934 58

220521 64

32634 10

286297 11

I get the following error:

"Too many columns in whitelist newhybs.list' at line 1"

Thanks for your help,

Norah Saarman