direct mapping between chormosomal positions between hg19 and hg38 dbSNP positions
1
Hi,
Is there a direct 1:1 mapping of positions between say dbSNP build 151 HG19 positions and HG38 positions available somewhere?
Thanks,
Jyoti
assembly
alignment
genome
snp
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using mysql/ucsc:
$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg38 -e 'select S1.name,S1.chrom,S1.chromStart,S1.chromEnd,S2.chrom,S2.chromStart,S2.chromEnd from hg19.snp150 as S1 , hg38.snp150 as S2 where S1.name=S2.name limit 20'
+--------------+-------+------------+----------+-------+------------+----------+
| name | chrom | chromStart | chromEnd | chrom | chromStart | chromEnd |
+--------------+-------+------------+----------+-------+------------+----------+
| rs775809821 | chr1 | 10019 | 10020 | chr1 | 10019 | 10020 |
| rs978760828 | chr1 | 10038 | 10039 | chr1 | 10038 | 10039 |
| rs1008829651 | chr1 | 10042 | 10043 | chr1 | 10042 | 10043 |
| rs1052373574 | chr1 | 10050 | 10051 | chr1 | 10050 | 10051 |
| rs892501864 | chr1 | 10054 | 10055 | chr1 | 10054 | 10055 |
| rs768019142 | chr1 | 10055 | 10055 | chr1 | 10055 | 10055 |
| rs1010989343 | chr1 | 10062 | 10063 | chr1 | 10062 | 10063 |
| rs1022805358 | chr1 | 10076 | 10077 | chr1 | 10076 | 10077 |
| rs62651026 | chr1 | 10107 | 10108 | chr1 | 10107 | 10108 |
| rs376007522 | chr1 | 10108 | 10109 | chr1 | 10108 | 10109 |
| rs796688738 | chr1 | 10128 | 10128 | chr1 | 10128 | 10128 |
| rs368469931 | chr1 | 10138 | 10139 | chr1 | 10138 | 10139 |
| rs144773400 | chr1 | 10144 | 10145 | chr1 | 10144 | 10145 |
| rs779258992 | chr1 | 10146 | 10147 | chr1 | 10146 | 10147 |
| rs371194064 | chr1 | 10149 | 10150 | chr1 | 10149 | 10150 |
| rs796884232 | chr1 | 10165 | 10165 | chr1 | 10165 | 10165 |
| rs201752861 | chr1 | 10176 | 10177 | chr1 | 10176 | 10177 |
| rs367896724 | chr1 | 10177 | 10177 | chr1 | 10177 | 10177 |
| rs201694901 | chr1 | 10179 | 10180 | chr1 | 10179 | 10180 |
| rs905327004 | chr1 | 10198 | 10199 | chr1 | 10198 | 10199 |
+--------------+-------+------------+----------+-------+------------+----------+
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Thanks that works. This is where I got the originals anyway. best, J
If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
PS. can I \T it so the output can be redirected?
just redirect the output like a standard cmd line, the formatting will be removed.