How to Convert Illumina Final Report File To Plink

Question

[g744695539]

Hi, all!

I only have one such file. How can I convert it to a format that plink can use?

[Header]
GSGT Version    2.0.4
Processing Date 2/14/2022 10:18 AM
Content         GSAMD-24v2-0_20024620_A1.bpm
Num SNPs        759993
Total SNPs      759993
Num Samples     1104
Total Samples   1104
[Data]
SNP Name        Sample Group    Sample Name     Sample ID       Sample Index    GC Score        Theta   R       B Allele Freq   Log R Ratio
1:100292476                     1       1       0.2752  0.205   0.962   0.0000  -0.0748
1:101064936                     1       1       0.2564  0.137   3.483   0.0000  0.2236
1:103380393                     1       1       0.8938  0.950   0.681   0.9889  -0.2339
1:104303716                     1       1       0.4682  0.970   0.751   1.0000  -0.1289
1:104864464                     1       1       0.2388  0.740   1.837   0.8692  0.1015
1:106737318                     1       1       0.8230  0.024   0.585   0.0000  -0.0870

[size_t]

try this tool: SNPchimpRepo

[g744695539]

Hi, I see that this tool requires two inputs, but I don’t have the SNP_Map (original from Illumina).

[size_t]

build a Map file by yourself, note that the SNP Name in the finalreport file must be included in the map file, otherwise an error will be reported when converting

[g744695539]

I downloaded the GSAMD-24v2-0_20024620_A1-b37.strand file from https://www.well.ox.ac.uk/~wrayner/strand/index.html and generated a map file. Then, based on the strand file, I added the Allele1 - Top and Allele2 - Top columns to the final report. For example, for 1:100292476, both Allele1 - Top and Allele2 - Top are A because BAF is 0. Similarly, for 1:104303716, both Allele1 - Top and Allele2 - Top are G. Please see if there is anything wrong

head GSAMD-24v2-0_20024620_A1-b37.SnpMap.txt
Index   Name    Chromosome  Position    SNP
1   1:100292476 1   100292476   [A/G]
2   1:101064936 1   101064936   [A/G]
3   1:103380393 1   103380393   [A/G]
4   1:104303716 1   104303716   [A/G]
5   1:104864464 1   104864464   [A/G]
...
164 1:156105002 1   156105002   [D/I]
167 1:156107472 1   156107465   [D/I]
168 1:156108399 1   156108399   [D/I]

[Header]
GSGT Version    2.0.4
Processing Date 2/14/2022 10:18 AM
Content         GSAMD-24v2-0_20024620_A1.bpm
Num SNPs        759993
Total SNPs      759993
Num Samples     1104
Total Samples   1104
[Data]
SNP Name        Sample Group    Sample Name     Sample ID       Sample Index    GC Score        Theta   R       B Allele Freq   Log R Ratio    Allele1 - Top    Allele2 - Top
1:100292476                     1       1       0.2752  0.205   0.962   0.0000  -0.0748    A    A
1:101064936                     1       1       0.2564  0.137   3.483   0.0000  0.2236    A    A
1:103380393                     1       1       0.8938  0.950   0.681   0.9889  -0.2339    A    G
1:104303716                     1       1       0.4682  0.970   0.751   1.0000  -0.1289    G    G
1:104864464                     1       1       0.2388  0.740   1.837   0.8692  0.1015    A    G

[Yan]

Hi there, I have the same problem. did you success using SNPchimpRepo? Thanks!

[GenoMax]

Note sure if this would be useful: https://--gist.github.com/RyanSchu/301ea0a77a21414391b54193dfcea9e0

Please take out the -- before gist in the link to see code. Added that so biostars does not render the code in-line since it is not my code.