convert_bim_allele.pl help

I am using Illumina data.

rs646776 in dbSNP is C>T. In my data it is G>A I have created a SNPTable.txt file (the line for rs646776 looks like this): rs646776 [A/G] TOP TOP

I tried with --outtype dbsnp: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype dbsnp --outfile converted_allele.bim but I get the same G A genotypes

I'm thinking I need to do --outtype forward: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype forward --outfile converted_allele.bim --strandfile my_strandfile.txt

I made my_strandfile.txt from taking the rsID and strand information from the Illumina manifest.csv so: rs646776 -

This seems to run successfully but when I check the now converted_allele.bim $ grep rs646776 converted_allele.bim 1 rs646776 129.6542 109818530 G A

I'm still getting the same genotype as before? Do you know how I convert this to the same as dbSNP e.g. C>T

Did you use the exported data from Illumina genome studio? It seems that you are just using dbSNP data? In that case, there is no need to convert_bim_allele.pl tool. "dbsnp" is not the best out type to use, because it contains a minor fraction of reverse strand SNP information as well. So if you have TOP allele, it is best that you convert to forward strand allele for a specific genome build.

Annoar's hg19_avsnp147 has no strand information in. You have to use dbsnp147 directly from UCSC genome browser as you have done. It is likely that this SNP is obsolete, or too new, so it is not included in the snp147 file. Try a more recent version to see if you can find it.

On Sun, Jan 23, 2022 at 8:04 PM zoeward-nz @.***> wrote:

I am using Illumina data.

rs646776 in dbSNP is C>T. In my data it is G>A I have created a SNPTable.txt file (the line for rs646776 looks like this): rs646776 [A/G] TOP TOP

I tried with --outtype dbsnp: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype dbsnp --outfile converted_allele.bim but I get the same G A genotypes

I'm thinking I need to do --outtype forward: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype forward --outfile converted_allele.bim --strandfile my_strandfile.txt

I tried to make a my_strandflle.txt by downloading the hg19_avsnp147.txt from ANNOVAR but doesn't have strand information in it?? (the line for rs646776 looks like this): 1 109818530 109818530 C T rs646776

I tried downloading the snp147.txt.gz from here: http://hgdownload.soe.ucsc.edu/goldenPath/galGal5/database/

which does appear to have strand information in it but this doesn't have my rs646776 present.

Can you help with the correct strandfile??

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Hi Kai,

Thanks for your speedy reply as I'm totally stuck on this.

I want my data to reflect the genotypes that are in dbSNP. If this is also achieved with the forward outtype then I'm happy to this.

At the moment my data does NOT reflect what is in dnSNP. The example snp that I used is C>T in dbSNP and G>A in my data

On Mon, Jan 24, 2022, 18:06 Kai Wang @.***> wrote:

Did you use the exported data from Illumina genome studio? It seems that you are just using dbSNP data? In that case, there is no need to convert_bim_allele.pl tool. "dbsnp" is not the best out type to use, because it contains a minor fraction of reverse strand SNP information as well. So if you have TOP allele, it is best that you convert to forward strand allele for a specific genome build.

Annoar's hg19_avsnp147 has no strand information in. You have to use dbsnp147 directly from UCSC genome browser as you have done. It is likely that this SNP is obsolete, or too new, so it is not included in the snp147 file. Try a more recent version to see if you can find it.

On Sun, Jan 23, 2022 at 8:04 PM zoeward-nz @.***> wrote:

I am using Illumina data.

rs646776 in dbSNP is C>T. In my data it is G>A I have created a SNPTable.txt file (the line for rs646776 looks like this): rs646776 [A/G] TOP TOP

I tried with --outtype dbsnp: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype dbsnp --outfile converted_allele.bim but I get the same G A genotypes

I'm thinking I need to do --outtype forward: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype forward --outfile converted_allele.bim --strandfile my_strandfile.txt

I tried to make a my_strandflle.txt by downloading the hg19_avsnp147.txt from ANNOVAR but doesn't have strand information in it?? (the line for rs646776 looks like this): 1 109818530 109818530 C T rs646776

I tried downloading the snp147.txt.gz from here: http://hgdownload.soe.ucsc.edu/goldenPath/galGal5/database/

which does appear to have strand information in it but this doesn't have my rs646776 present.

Can you help with the correct strandfile??

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dbSNP has numerous errors and by definition, dbSNP's rsid is a locus identifier only (the same dbSNP record can mean a dozen completely different mutations), not a mutation identifier, so it can be problematic to match dbsnp since information in dbsnp is not identifiable. Using forward strand for a specific genome build (such as hg19 and hg38) is really the only way to identify a mutation.

On Mon, Jan 24, 2022 at 2:48 PM zoeward-nz @.***> wrote:

Hi Kai,

Thanks for your speedy reply as I'm totally stuck on this.

I want my data to reflect the genotypes that are in dbSNP. Of this is achieved with the forward outtype then I'm happy to this also.

At the moment my data does NOT reflect what is in dnSNP. The example snp that I used is C>T in dbSNP and G>A in my data

On Mon, Jan 24, 2022, 18:06 Kai Wang @.***> wrote:

Did you use the exported data from Illumina genome studio? It seems that you are just using dbSNP data? In that case, there is no need to convert_bim_allele.pl tool. "dbsnp" is not the best out type to use, because it contains a minor fraction of reverse strand SNP information as well. So if you have TOP allele, it is best that you convert to forward strand allele for a specific genome build.

Annoar's hg19_avsnp147 has no strand information in. You have to use dbsnp147 directly from UCSC genome browser as you have done. It is likely that this SNP is obsolete, or too new, so it is not included in the snp147 file. Try a more recent version to see if you can find it.

On Sun, Jan 23, 2022 at 8:04 PM zoeward-nz @.***> wrote:

I am using Illumina data.

rs646776 in dbSNP is C>T. In my data it is G>A I have created a SNPTable.txt file (the line for rs646776 looks like this): rs646776 [A/G] TOP TOP

I tried with --outtype dbsnp: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype dbsnp --outfile converted_allele.bim but I get the same G A genotypes

I'm thinking I need to do --outtype forward: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype forward --outfile converted_allele.bim --strandfile my_strandfile.txt

I tried to make a my_strandflle.txt by downloading the hg19_avsnp147.txt from ANNOVAR but doesn't have strand information in it?? (the line for rs646776 looks like this): 1 109818530 109818530 C T rs646776

I tried downloading the snp147.txt.gz from here: http://hgdownload.soe.ucsc.edu/goldenPath/galGal5/database/

which does appear to have strand information in it but this doesn't have my rs646776 present.

Can you help with the correct strandfile??

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Thanks Kai,

So if I set convert_bim_allele.pl to --outype forward All of the genotypes in my data will be referencing the forward strand of the sequence?

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On Tue, Jan 25, 2022 at 4:10 PM Kai Wang @.***> wrote:

dbSNP has numerous errors and by definition, dbSNP's rsid is a locus identifier only (the same dbSNP record can mean a dozen completely different mutations), not a mutation identifier, so it can be problematic to match dbsnp since information in dbsnp is not identifiable. Using forward strand for a specific genome build (such as hg19 and hg38) is really the only way to identify a mutation.

On Mon, Jan 24, 2022 at 2:48 PM zoeward-nz @.***> wrote:

Hi Kai,

Thanks for your speedy reply as I'm totally stuck on this.

I want my data to reflect the genotypes that are in dbSNP. Of this is achieved with the forward outtype then I'm happy to this also.

At the moment my data does NOT reflect what is in dnSNP. The example snp that I used is C>T in dbSNP and G>A in my data

On Mon, Jan 24, 2022, 18:06 Kai Wang @.***> wrote:

Did you use the exported data from Illumina genome studio? It seems that you are just using dbSNP data? In that case, there is no need to convert_bim_allele.pl tool. "dbsnp" is not the best out type to use, because it contains a minor fraction of reverse strand SNP information as well. So if you have TOP allele, it is best that you convert to forward strand allele for a specific genome build.

Annoar's hg19_avsnp147 has no strand information in. You have to use dbsnp147 directly from UCSC genome browser as you have done. It is likely that this SNP is obsolete, or too new, so it is not included in the snp147 file. Try a more recent version to see if you can find it.

On Sun, Jan 23, 2022 at 8:04 PM zoeward-nz @.***> wrote:

I am using Illumina data.

rs646776 in dbSNP is C>T. In my data it is G>A I have created a SNPTable.txt file (the line for rs646776 looks like this): rs646776 [A/G] TOP TOP

I tried with --outtype dbsnp: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype dbsnp --outfile converted_allele.bim but I get the same G A genotypes

I'm thinking I need to do --outtype forward: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype forward --outfile converted_allele.bim --strandfile my_strandfile.txt

I tried to make a my_strandflle.txt by downloading the hg19_avsnp147.txt from ANNOVAR but doesn't have strand information in it?? (the line for rs646776 looks like this): 1 109818530 109818530 C T rs646776

I tried downloading the snp147.txt.gz from here: http://hgdownload.soe.ucsc.edu/goldenPath/galGal5/database/

which does appear to have strand information in it but this doesn't have my rs646776 present.

Can you help with the correct strandfile??

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Yes, if the snptable file is correct for the specific genome coordinate that you are using.

On Mon, Jan 24, 2022 at 11:06 PM zoeward-nz @.***> wrote:

Thanks Kai,

So if I set convert_bim_allele.pl to --outype forward All of the genotypes in my data will be referencing the forward strand of the sequence?

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On Tue, Jan 25, 2022 at 4:10 PM Kai Wang @.***> wrote:

dbSNP has numerous errors and by definition, dbSNP's rsid is a locus identifier only (the same dbSNP record can mean a dozen completely different mutations), not a mutation identifier, so it can be problematic to match dbsnp since information in dbsnp is not identifiable. Using forward strand for a specific genome build (such as hg19 and hg38) is really the only way to identify a mutation.

On Mon, Jan 24, 2022 at 2:48 PM zoeward-nz @.***> wrote:

Hi Kai,

Thanks for your speedy reply as I'm totally stuck on this.

I want my data to reflect the genotypes that are in dbSNP. Of this is achieved with the forward outtype then I'm happy to this also.

At the moment my data does NOT reflect what is in dnSNP. The example snp that I used is C>T in dbSNP and G>A in my data

On Mon, Jan 24, 2022, 18:06 Kai Wang @.***> wrote:

Did you use the exported data from Illumina genome studio? It seems that you are just using dbSNP data? In that case, there is no need to convert_bim_allele.pl tool. "dbsnp" is not the best out type to use, because it contains a minor fraction of reverse strand SNP information as well. So if you have TOP allele, it is best that you convert to forward strand allele for a specific genome build.

Annoar's hg19_avsnp147 has no strand information in. You have to use dbsnp147 directly from UCSC genome browser as you have done. It is likely that this SNP is obsolete, or too new, so it is not included in the snp147 file. Try a more recent version to see if you can find it.

On Sun, Jan 23, 2022 at 8:04 PM zoeward-nz @.***> wrote:

I am using Illumina data.

rs646776 in dbSNP is C>T. In my data it is G>A I have created a SNPTable.txt file (the line for rs646776 looks like this): rs646776 [A/G] TOP TOP

I tried with --outtype dbsnp: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype dbsnp --outfile converted_allele.bim but I get the same G A genotypes

I'm thinking I need to do --outtype forward: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype forward --outfile converted_allele.bim --strandfile my_strandfile.txt

I tried to make a my_strandflle.txt by downloading the hg19_avsnp147.txt from ANNOVAR but doesn't have strand information in it?? (the line for rs646776 looks like this): 1 109818530 109818530 C T rs646776

I tried downloading the snp147.txt.gz from here: http://hgdownload.soe.ucsc.edu/goldenPath/galGal5/database/

which does appear to have strand information in it but this doesn't have my rs646776 present.

Can you help with the correct strandfile??

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Then I don't think it has worked?

After running convert_bim_allele.pl with --outtype forward I get (using one snp as an example): 19 rs1122608 31.58171 11163601 A C

On hg19 position 19:11163601 the forward strand is a G

On Tue, Jan 25, 2022 at 5:37 PM Kai Wang @.***> wrote:

Yes, if the snptable file is correct for the specific genome coordinate that you are using.

On Mon, Jan 24, 2022 at 11:06 PM zoeward-nz @.***> wrote:

Thanks Kai,

So if I set convert_bim_allele.pl to --outype forward All of the genotypes in my data will be referencing the forward strand of the sequence?

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On Tue, Jan 25, 2022 at 4:10 PM Kai Wang @.***> wrote:

dbSNP has numerous errors and by definition, dbSNP's rsid is a locus identifier only (the same dbSNP record can mean a dozen completely different mutations), not a mutation identifier, so it can be problematic to match dbsnp since information in dbsnp is not identifiable. Using forward strand for a specific genome build (such as hg19 and hg38) is really the only way to identify a mutation.

On Mon, Jan 24, 2022 at 2:48 PM zoeward-nz @.***> wrote:

Hi Kai,

Thanks for your speedy reply as I'm totally stuck on this.

I want my data to reflect the genotypes that are in dbSNP. Of this is achieved with the forward outtype then I'm happy to this also.

At the moment my data does NOT reflect what is in dnSNP. The example snp that I used is C>T in dbSNP and G>A in my data

On Mon, Jan 24, 2022, 18:06 Kai Wang @.***> wrote:

Did you use the exported data from Illumina genome studio? It seems that you are just using dbSNP data? In that case, there is no need to convert_bim_allele.pl tool. "dbsnp" is not the best out type to use, because it contains a minor fraction of reverse strand SNP information as well. So if you have TOP allele, it is best that you convert to forward strand allele for a specific genome build.

Annoar's hg19_avsnp147 has no strand information in. You have to use dbsnp147 directly from UCSC genome browser as you have done. It is likely that this SNP is obsolete, or too new, so it is not included in the snp147 file. Try a more recent version to see if you can find it.

On Sun, Jan 23, 2022 at 8:04 PM zoeward-nz @.***> wrote:

I am using Illumina data.

rs646776 in dbSNP is C>T. In my data it is G>A I have created a SNPTable.txt file (the line for rs646776 looks like this): rs646776 [A/G] TOP TOP

I tried with --outtype dbsnp: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype dbsnp --outfile converted_allele.bim but I get the same G A genotypes

I'm thinking I need to do --outtype forward: $ perl convert_bim_allele.pl my.bim SNPTable.txt --intype top --outtype forward --outfile converted_allele.bim --strandfile my_strandfile.txt

I tried to make a my_strandflle.txt by downloading the hg19_avsnp147.txt from ANNOVAR but doesn't have strand information in it?? (the line for rs646776 looks like this): 1 109818530 109818530 C T rs646776

I tried downloading the snp147.txt.gz from here: http://hgdownload.soe.ucsc.edu/goldenPath/galGal5/database/

which does appear to have strand information in it but this doesn't have my rs646776 present.

Can you help with the correct strandfile??

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WGLab / GenGen

convert_bim_allele.pl help #10