1. What is “left join (loj)” mode?
VarNote can perform a “left outer join”. That is, for each feature in query report each overlap with database. If no overlaps or desired items are found, report an empty (.) feature for such feature.
2. Why some of my query variants cannot retrieve allele-specific annotation from databases with over two alleles for some variants, such as gnomAD?
Since diversity of variant allele representation in current applications, some alleles may different and represent same consequence, particular for combined allele sites. It is recommended that both the variants in the query and each database are normalized and decomposed in order to ensure that both variant sites and alleles are properly matched when performing allele-specific annotation.
3. If I have reference and alternative alleles in my query, but I only want to perform region-based annotation regardless of allele information.
VarNote has a force overlap mode in the annotation function, which force the program to omit REF and ALT matching and allele specific feature extraction. Please check the program usage page.
4. Whether VarNote supports reference and alternative alleles from reverse strand of genome?
VarNote requires that allele information among query and annotation databases should be consistent strand.
5. Can a compressed query file be processed in parallel?
Yes, it can. VarNote supports position-sorted compressed file including gzip, block gzip and allows multi-threading for these formats.
6. Can I run VarNote on my Mac laptop in parallel?
Yes, it can. VarNote is a memory-efficient program.
7. How do I report bugs or suggest functions to VarNote?
You are welcomed to report bugs or suggest functions via github issues channel (https://github.com/mulinlab/VarNote/issues).
1. What is “left join (loj)” mode? VarNote can perform a “left outer join”. That is, for each feature in query report each overlap with database. If no overlaps or desired items are found, report an empty (.) feature for such feature.
2. Why some of my query variants cannot retrieve allele-specific annotation from databases with over two alleles for some variants, such as gnomAD? Since diversity of variant allele representation in current applications, some alleles may different and represent same consequence, particular for combined allele sites. It is recommended that both the variants in the query and each database are normalized and decomposed in order to ensure that both variant sites and alleles are properly matched when performing allele-specific annotation.
3. If I have reference and alternative alleles in my query, but I only want to perform region-based annotation regardless of allele information. VarNote has a force overlap mode in the annotation function, which force the program to omit REF and ALT matching and allele specific feature extraction. Please check the program usage page.
4. Whether VarNote supports reference and alternative alleles from reverse strand of genome? VarNote requires that allele information among query and annotation databases should be consistent strand.
5. Can a compressed query file be processed in parallel? Yes, it can. VarNote supports position-sorted compressed file including gzip, block gzip and allows multi-threading for these formats.
6. Can I run VarNote on my Mac laptop in parallel? Yes, it can. VarNote is a memory-efficient program.
7. How do I report bugs or suggest functions to VarNote? You are welcomed to report bugs or suggest functions via github issues channel (https://github.com/mulinlab/VarNote/issues).