After mapping one Sanger sequence read (about 900bp) to hg19 using blastn, How can I get variants presented as reference-based position and base change with the blastn output file?

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li lilingdu ▴ 450

@li-lilingdu-1884

Last seen 6.5 years ago

Hi,

After mapping one Sanger sequence read (about 900bp) to hg19 using blastn of NCBI, How can I get variants presented as reference-based position and base change with the blastn output file such as XML output or asn1 output?

For example,

Query  7         GAAAG--AACAGGCT-ACAATTTTGGACTCTGGTCTCTTGGGGCTACATTGAGCATTGAC  63
                 |||||  |||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct  27108850  GAAAGAAAACAGGCTAACAATTTTGGACTCTGGTCTCTTGGGGCTACATTGAGCATTGAC  27108909

I want get the first variant presented as: chr9:27108854-27108854:G-GAA, does there exist any tools in packages such as Biostrings and GenomicAlignments to do this?