Variant calling from FASTA file

Question

[User000]

Dear all,

I have a fasta file contatining marker ID's:

>marker1
AGCTGGGTGTCGTTGATCTTCAGGTCCTTCTGGATGTACAGCGACGCTCCActcatcacg
ccgatgtcgtagccgaggaggatggaggtcatggaggcgag
>marker2
CTCGTCGGTTTCGACCACCATGTTGTCATGGGCATAGCATAGTGAACTCCACTCACAGCT
AAAAAGGAACGGTGCCTGCCTTCTTTTCAGTATCTAATTAC
>markern
CATCTAATTTGTTGGACGGGGATATGCTGGGAAAACGAAGAGCAAATCTGTGCCCACTGT
GCTGGTCGCTGCAGAATCTATTCCCCATTATGTTGCCTGTT

I would like to align these markers against the reference genome and find the position of variant for every single marker if there any:

#CHROM  POS ID  REF ALT
chr1    1101439 marker1 C   A
chr1    1104710 marker2 A   T
chr1    1104748 markern C   T

I am trying to use both bwa/bowtie to align and bcftools/gatk to call variants, but I do not know how to include also the marker ID in the vcf file? OR MAY BE THIS IS POSSIBLE BY PARSING THE BLAST OUTPUT?

Answer 1

[JC]

if you want to add the markerID, it's better to align with Blast and parse the result to generate the custom VCF

[User000]

any hints how to do this? thanks

[User000]

I will this and see if it works: Find Mismatch And Gap Positions

Answer 2

[User000]

This wonderful program solved my problem (Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030):

http://lindenb.github.io/jvarkit/BlastNToSnp.html