Creating an avinput from avsnp file error about doc-annovar

[kaichop]

avsnp is not supported. You could simply "grep -w -f rslist.txt hg19_avsnp147.txt" to generate the desired file.

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On Thu, Mar 30, 2017 at 11:47 AM, Robert Butler ***@***.***> wrote: I am having an issue with convert2annovar.pl from an rsID list. Using the following: convert2annovar.pl -format rsid rslist.txt -dbsnpfile ${annovar}humandb/hg19_avsnp147.txt > rslist.avinput I get: NOTICE: Scanning dbSNP file /opt/annovar/humandb/hg19_avsnp147.txt... Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 1. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 1. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 1. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 1. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 2. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 2. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 2. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 2. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 3. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 3. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 3. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 3. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 4. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 4. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 4. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 4. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 5. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 5. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 5. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 5. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 6. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 6. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 6. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 6. Use of uninitialized value $class in string eq at /opt/annovar/ convert2annovar.pl line 1022, line 7. And so forth for all lines (I stopped checking after more than a million lines). Input file looks like: rs150829393 rs112039851 rs1800562 rs200401432 rs118161496 rs1799945 And does the same with or without the rs prefix. Is there a different dbSNP file to use? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#16>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuP6q940-UQU4P8MM0fgd42OpcVfBks5rq86ZgaJpZM4MujZg> .

[rbutleriii]

Worked, perhaps in the next version of convert2annovar.pl it will simply grep, as snp138 is from 2014.

[rbutleriii]

FYI for long lists I used a perl block to take an rsID list mapped to hash keys (%rsIDbatch) and make the avinput file:

open(IN7, "$anno_avsnp_file");
open(OUT4, ">rslist.avinput");
while (my $line = <IN7>){
	chomp $line;
	$line =~ /rs(\d+)$/;
		if (exists $rsIDbatch{$1}){
			print OUT4 "$line\n";
		} else { next; }
}
close IN7;
close OUT4;

Massively shortens execution time. Could be useful for others, or for generating inputs to InterVar.

[kaichop]

Thank you for the comments. This function will be added in the next version of ANNOVAR.

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On Tue, Apr 4, 2017 at 5:03 PM, Robert Butler ***@***.***> wrote: FYI for long lists I used a perl block to take an rsID list mapped to hash keys (%rsIDbatch) and make the avinput file: open(IN7, "$anno_avsnp_file"); open(OUT4, ">rslist.avinput"); while (my $line = ){ chomp $line; $line =~ /rs(\d+)$/; if (exists $rsIDbatch{$1}){ print OUT4 "$line\n"; } else { next; } } close IN7; close OUT4; Massively shortens execution time. Could be useful for others, or for generating inputs to InterVar. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#16 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuEPdfTJcy2IKR5VAIF0u_uzr642bks5rsrAdgaJpZM4MujZg> .