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?


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