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Mismatch header after generating reference from FastaAlternateReferenceMaker

MilkMilk Member

I try to use the command "FastaAlternateReferenceMaker" to build a new genome reference from FASTA+VCF. However, the header format is changed from >AABL01000001 to >1 AABL01000001:1 (the number was added before the chromosome name). My question is that there are any commands using to replace this header back to the same as old header in FASTA file?
The commands I used are:
java -jar /GenomeAnalysisTK-3.8/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R aaa.fasta -o aaa_new.fasta -V bbb.vcf




  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    It looks as if the output fasta headers add a sequential number which is what you are seeing. The tool does not have a way to remove those sequential numbers but here is an option that you can modify to remove the sequential numbers.

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