How to append fasta files

[FrankiB]

Hi,

I have a series of snp and indels (csv format) for which I know the exact location on the the human genome (chromosome# and nucleotide position) and I would like to append the human genome (fasta format) by inserting the snp/indels (from the csv file) at the genomic position describe in the csv file.

Is anyone can suggest me a computer tool that could help? I have some basic skills (very very basic skills) in programming with python but this one would be too difficult for me to realize.

Thank you for your help

[dpryan]

You're not looking to "append" (which would put this information at the end), but rather simply modify the original (presumably writing the modified version to a new file). An example program would be GATK's FastaAlternateReferenceMaker.

[FrankiB]

Ok. Thank you.

But the command line to run FastaAlternateReferenceMaker requires a .intervals file (that one has been produced using the GATK pipeline) as input. Also I performed the variant calling using Varscan2. So the number of intervals in the .intervals file doesn't necessarily match the number of variants called by Varscan2. Is it a problem?

I tried althought the unmatched numbers of variants and intervals, and got this output (it's only a infinite part of it):

>1
GC
>2
CA
>3
AG
>4
AAAC
...

I was surprised because I thought that the output would be a fasta file with modified sequences (in my case the input was the full human genome, each sequence being a chromosome)... I ended up with sequences of 2 or few nucleotides long...

[dpryan]

The interval file just specifies particular ranges to look at. For the whole genome, just specify all of the chromosomes.

[FrankiB]

So for the whole genome, I do not need the .intervals file in the input command line...

[dpryan]

Whether the command itself will allow it or not I don't know. If it doesn't complain when you just ignore that option then there's presumably no need. Otherwise, just input the bounds of each chromosome (yes, this would seem rather silly).