variants that have multiple alleles

Question

[priyag8179]

I need a couple of examples of variants that have multiple alleles. For example, a substitution at a genomic location where there are two possible base pair substitutions, such as T>G or T>C. Ideally I'd like to see this example in dbSNP, NHLBI ESP, and ExAC

[priyag8179]

I am new, and I do not understand this, will you please explain??

[priyag8179]

And these variants are from DbSNP, What about NHLBI ESP, and ExAC any one can help?

[Pierre Lindenbaum]

Don't post your comments as new answers.

[priyag8179]

And I am specifically looking for substitution, if you follow HGVS then a substitution at a genomic location where there are two possible base pair substitutions, such as T>G or T>C

[Devon Ryan]

All but two of the examples Pierre showed are single-base substitutions.

Answer 1

[Pierre Lindenbaum]

$ curl -s  "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz" |\
gunzip -c | awk -F '\t' '(index($5,",")!=0)' |head
1    10493    rs199606420    C    A,G    .    .    RS=199606420;RSPOS=10493;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050000020005000002000100;WGT=1;VC=SNV;R5;ASP
1    15274    rs62636497    A    G,T    .    .    RS=62636497;RSPOS=15274;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050000080005140126000100;WGT=1;VC=SNV;INT;ASP;VLD;GNO;KGPhase3
1    49156    rs372792512    C    A,T    .    .    RS=372792512;RSPOS=49156;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997,.;COMMON=0
1    49404    rs2531246    C    A,T    .    .    RS=2531246;RSPOS=49404;dbSNPBuildID=100;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP
1    67223    rs78676975    C    A,T    .    .    RS=78676975;RSPOS=67223;dbSNPBuildID=131;SSR=0;SAO=0;VP=0x050000020005040126000100;WGT=1;VC=SNV;R5;ASP;VLD;GNO;KGPhase3;CAF=0.9988,.,0.001198;COMMON=1
1    72297    rs369919718    G    GTTA,GTAT    .    .    RS=369919718;RSPOS=72298;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP;CAF=0.9958,.,0.004193;COMMON=1
1    87027    rs375864588    A    G,T    .    .    RS=375864588;RSPOS=87027;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,.,0.0001997;COMMON=0
1    99043    rs12184295    T    A,G    .    .    RS=12184295;RSPOS=99043;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,.,0.0001997;COMMON=0
1    99665    rs368526587    C    A,T    .    .    RS=368526587;RSPOS=99665;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.999,0.0009984,.;COMMON=0
1    120994    rs71218814    AAT    A,ATAT    .    .    RS=71218814;RSPOS=120995;dbSNPBuildID=130;SSR=0;SAO=0;VP=0x050100080005000102000200;WGT=1;VC=DIV;SLO;INT;ASP;GNO

[Pierre Lindenbaum]

curl: download a variant call format (VCF) file from the NCBI/dbsnp

gunzip: unzip a stream on the fly

awk: using a tab as a delimiter, get the line where the 5th column (ALT alleles) contains a comma

head: print the first 10 lines