Hi, everyone! First, ASA from _ILLUMINA_ means Asian Screening Array. I couldn't find this product on _ILLUMINA_ websit. However ASA seems to be Asian version of GSA, GSA:
GSA is a next-generation genotyping array for population-scale genetics, variant screening, pharmacogenomics studies, and precision medicine research.
I got a ASA result demo and want to match those SNP result to dbSNP. Result contains:
20180423_2s_ASA_v1_FinalReport_3rdparty.txt
20180423_2s_ASA_v1_FinalReport_forward.csv
20180423_2s_ASA_v1_FinalReport_standard.txt
3rdparty.txt is SNP report using Top/Bot system design by _ILLUMINA_
forward.csv is SNP report using Forward/Reverse strand system design by dbSNP
standard.txt is SNP report with all details
It seems I can grab SNP from forward.csv then search on dbSNP. (I think this file name means all result is forward strand, right?). Here is the result file format:
- header
>[Header]
GSGT Version,2.0.3
Processing Date,4/23/2018 4:07 PM
Content,,ASA-24v1-0-Consort_20022506_A2.bpm
Num SNPs,698500
Total SNPs,698500
Num Samples,2
Total Samples,2
[Data]
,S1,S2
question: which reference was applied? GRCh38 or hg19?
here is lines in file:
some lines are like:
1:12061471,DD|0.4341,DD|0.6089
1:156084831,GG|0.4954,GG|0.4954some lines are like:
ACADSB:c.303+3A>G,AA|0.4154,AA|0.4154
ATM:c.3245_3247delATCinsTGAT,CC|0.5119,CC|0.5119
CNGB3:c.991-3T>G,AA|0.4712,AA|0.4712
COL4A3:c.4420_4424delCTTTT,II|0.6556,II|0.6556some lines are like
ilmnseq_1:110198788,TT|0.4876,TT|0.4876
ilmnseq_1:110201667,CC|0.5276,CC|0.5276some lines are like
IlmnSeq_rs17002852,AA|0.2354,AA|0.2354
IlmnSeq_rs17002853,AA|0.1771,AA|0.1771
ilmnseq_rs17146904.2_F2BT,TT|0.3485,TT|0.3485
- some lines are like
rs111033242,CC|0.7732,CC|0.7732
rs111033252,GG|0.3078,GG|0.3078
seq-rs398123106,CC|0.1899,CC|0.1899
seq-rs398123108,GG|0.2065,GG|0.2065
some lines are like
Y:9485180,AA|0.8100,AG|0.3151
Y:9829235,TT|0.7604,TC|0.3355and more...
This means all those SNP are not named by the same way, maybe from different source. So how could I match those SNP to dbSNP? Any help would be appreciate, thanks!
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I think you need to ask Illumina. They sold you this product, they should support you with using it.