Timeline for update dbSNP ID
Current License: CC BY-SA 4.0
14 events
| when toggle format | what | by | license | comment | |
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| Apr 23, 2020 at 18:50 | comment | added | Geraldine_VdAuwera | Keep in mind that the different names sometimes correspond to different genome builds, so you should make absolutely sure that you are using the right (compatible) reference genome build before doing this. Eg you can't use a dbsnp set from b37 with a callset made using hg38 and vice versa. | |
| May 13, 2018 at 12:34 | vote | accept | Lot_to_learn | ||
| May 13, 2018 at 12:32 | comment | added | Lot_to_learn | A little correction in my previous comment. I don't know why, when I checked no. of rs ID's using grep, it shows big number but gatk tool shows very less known rs ID.So when I use latest version of dbSNP I found very less known and most of the mutations are novel according to gatk variantEval. When I checked, I found that its reference is GRC38. So I use 2017 version of dbSNP. Now I am getting lot more known variants in variantEval. Now I am OK with 2017th version of dbSNP. Thanks. | |
| May 12, 2018 at 12:29 | comment | added | terdon♦ |
@Lot_to_learn did you use the very latest edited version of my answer? The first had a couple of problems. To check, make sure that you have chrMT, chrY and chrX in the file.
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| May 12, 2018 at 9:26 | vote | accept | Lot_to_learn | ||
| May 13, 2018 at 12:34 | |||||
| May 12, 2018 at 9:26 | comment | added | Lot_to_learn | I have found more rs IDs from new dbSNP as comparison to old one. For one patient I got 3200 approx new rs IDs. Although I was expecting more new rs IDs. Thanks. This is working well. | |
| May 10, 2018 at 13:21 | history | edited | terdon♦ | CC BY-SA 4.0 |
added 16 characters in body
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| May 10, 2018 at 12:06 | comment | added | terdon♦ |
@Lot_to_learn please see the updated answer. The first version would not have corrected the names for chrX and chrY.
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| May 10, 2018 at 12:05 | history | edited | terdon♦ | CC BY-SA 4.0 |
deleted 19 characters in body
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| May 10, 2018 at 12:00 | comment | added | terdon♦ |
@Lot_to_learn whoops, yes sorry. GRC uses numbers only, it's the hg19 and hg38 that use chr. Answer edited. Also, where are you downloading these files from?
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| May 10, 2018 at 11:58 | history | edited | terdon♦ | CC BY-SA 4.0 |
deleted 3 characters in body
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| May 10, 2018 at 11:53 | comment | added | Lot_to_learn |
@heathobrien, @terdon : A little clarification here. I have downloded dbsnp_138.hg19.vcf.gz which use chr prefix and in file All_20170710 from GRC contains number only.
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| May 10, 2018 at 11:31 | history | edited | heathobrien | CC BY-SA 4.0 |
fixed mitochondrial chromosome naming
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| May 10, 2018 at 11:24 | history | answered | terdon♦ | CC BY-SA 4.0 |