FastaAlternateReferenceMaker Consensus sequence header
I am using FastaAlternateReferenceMaker to create consensus sequences as follows:
java -Xmx12g -jar /GenomeAnalysisTK-2.7-4-g6f46d11/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R /Reference/chromosome.1.fa -o /Output/consensus.1.fa --variant /VCF/chromosome1.vcf -L /Interval/chromosome.1.list
This command line produces a single fasta file including consensus sequences for the intervals provided in the list file.
(1) Presumably, sequence header for each sequence in the consensus fasta file corresponds to the contig name in the master reference file. Is there any way to modify the command line to print, say, the interval as the sequence header instead of the contig name?
Note: I can feed the program one interval at a time and name the output file accordingly, however, I'd like to stick to submitting my query per one chromosome at a time for the sake of saving up time.
(2) Number of sequences in the consensus fasta do not match the number of non-overlapping intervals in the input list. I would think that this is because some intervals are variant-free and therefore no alternate reference is reported for them. Do you confirm this is the case? I cannot easily check because the issue mentioned in (1).