I couldn't find relevant information. I hope it's not duplicate.
I have resequencing data for two maize lines (BAM and VCF files).
I want to extract sequences (fasta) for several genes (I have also GFF3 file with annotation data) from reference genome and corresponding sequences from resequencing data. I probably could use sequence identifiers, as they are in my files
Which tool allows to extract such data, and more generally to extract sequences for
a given variant type (SNP, indel, etc) and location (exon, intron, etc)?
I have resequencing data for two maize lines (BAM and VCF files).
I want to extract sequences (fasta) for several genes (I have also GFF3 file with annotation data) from reference genome and corresponding sequences from resequencing data. I probably could use sequence identifiers, as they are in my files
Which tool allows to extract such data, and more generally to extract sequences for
a given variant type (SNP, indel, etc) and location (exon, intron, etc)?
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