In the VCF format, there is the option for the ID field to have multiple semi-colon separated values. In theory, there could be two dbSNP rsIDs in a single line (i.e. two indels at chr:pos), but for programming purposes, that should not happen, correct? dbSNP has merged all variants for a given position to a common rsID?
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rrbutleriii
dbSNP has merged all variants for a given position to a common rsID?
I'm afraid no:
$ wget -q -O - "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/All_20180418.vcf.gz" | gunzip -c | grep -v "#" | cut -f 1,2 | uniq -d | head
1 10051
1 10055
1 10108
1 10109
1 10128
1 10132
1 10177
1 10228
1 10229
1 10235
.
$ wget -q -O - "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/All_20180418.vcf.gz" | gunzip -c | grep -v "#" | cut -f 1,2,3,4,5 | grep -w 10051 -m2
1 10051 rs1052373574 A G
1 10051 rs1326880612 A AC
Follow up:
So when parsing a vcf, would I then have to anticipate some variant callers giving me:
1 10051 rs1052373574;rs1326880612 A G,AC
I haven't ever seen that before, but I don't see anything to prohibit it.
Correct - nothing to prohibit it; however, it can cause issues for downstream analysis tools. Most will not support multi-allelic calls like this.
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