Hi, I'm Gabriel. I'm doing my thesis with SV's and vcf files. I'm doing a script to annotate SV's BND format in short annotation. One type of insertion is a single breakend INS and it's annotated like:
REF: A ; ALT: .AGTA(etc..).
Example:
The variant with gridss273b_534b ID starts with "." (this variant was annotated by SNPEff as INS.).
In python after using vcf_1kg=allel.vcf_to_dataframe(ruta_vcf,fields=['*'],exclude_fields=['FILTER_NO_RP', 'FILTER_SINGLE_ASSEMBLY','FILTER_ASSEMBLY_TOO_FEW_READ', 'FILTER_NO_ASSEMBLY', 'FILTER_NO_SR','FILTER_INSUFFICIENT_SUPPORT', 'FILTER_ASSEMBLY_BIAS','FILTER_ASSEMBLY_ONLY', 'FILTER_ASSEMBLY_TOO_SHORT','FILTER_SMALL_EVENT', 'FILTER_REF', 'FILTER_SINGLE_SUPPORT','FILTER_LOW_QUAL','FILTER_SnpSift'],alt_number=1)(OBS: ruta_vcf it's the PATH to the vcf. STRAND ,INS_LEN and INS_SEQ fields was added after to DataFrame in script)
ALT field is annotated as nan. I know that initial "." means missing value, and it is the reason to annotate as nan these fields. Can it be solved?. I'm using allel V1.3.2 and python 3.5.3.
Thank you.
Hi, I'm Gabriel. I'm doing my thesis with SV's and vcf files. I'm doing a script to annotate SV's BND format in short annotation. One type of insertion is a single breakend INS and it's annotated like: REF: A ; ALT: .AGTA(etc..). Example:
The variant with gridss273b_534b ID starts with "." (this variant was annotated by SNPEff as INS.).
In python after using 
ALT field is annotated as nan. I know that initial "." means missing value, and it is the reason to annotate as nan these fields. Can it be solved?. I'm using allel V1.3.2 and python 3.5.3.
Thank you.
vcf_1kg=allel.vcf_to_dataframe(ruta_vcf,fields=['*'],exclude_fields=['FILTER_NO_RP', 'FILTER_SINGLE_ASSEMBLY','FILTER_ASSEMBLY_TOO_FEW_READ', 'FILTER_NO_ASSEMBLY', 'FILTER_NO_SR','FILTER_INSUFFICIENT_SUPPORT', 'FILTER_ASSEMBLY_BIAS','FILTER_ASSEMBLY_ONLY', 'FILTER_ASSEMBLY_TOO_SHORT','FILTER_SMALL_EVENT', 'FILTER_REF', 'FILTER_SINGLE_SUPPORT','FILTER_LOW_QUAL','FILTER_SnpSift'],alt_number=1)(OBS: ruta_vcf it's the PATH to the vcf. STRAND ,INS_LEN and INS_SEQ fields was added after to DataFrame in script)