how to convert `v54.1.p1_1240K_public.snp` to aligned fasta format data?

[liamxg]

Dear @MatthewMah,

Could I know how to convert v54.1.p1_1240K_public.snp to aligned fasta format data? Thanks.

[MatthewMah]

I don't understand what you want to do. This is a list of single nucleotide polymorphisms, positions with reference and alternate allele possibilities. A fasta is a sequence, not aligned.

[liamxg]

Dear @MatthewMah,

I am sorry for the confusion.

can you transfer the snp file to the sequence file, and aligned based on the position?

[MatthewMah]

A SNP file is a series of positions. You take sequencing data and examine it at those positions. There is no sequencing data inherent in the SNP file.

If you want aligned sequencing data, that sounds like you want Sequence Alignment/Map (SAM/BAM/CRAM).

[liamxg]

Dear @MatthewMah,

I want a fasta format file like below:

>sample1
AAA---CCTT
>sample2
---CCTCCTT
>sample3
AAACTCCTT

[MatthewMah]

Then you need to start with sequencing data, not a SNP file.

[liamxg]

could snp transfer to fasta format data?