I am using FastaAlternateReferenceMaker to generate fasta reads with the indels I have in a VCF file. I am also using a bed file becaouse I need to create fasta reads from the specific start and end positions.

In general, I get what I need but the problem appears when I have regions in my bed file that overlap

chr19   33301307    33301599
chr19   33301556    33301805
chr19   33301647    33301946
chr19   33301898    33302195
chr19   33302152    33302440

which returns this

>39 chr19:33301308-33302440
TGGCCCAGGGCGGTCCCACAGCCGCGCGCCTCACGCGCAGTTGCCCATGGCCTGACCAAG
GAGCTCTCTGGCAGCTGGCGGAAGATGCCCCGCAGCGTGTCCAGTTCGCGGCTCAGCTGT
TCCACCCGCTTGCGCAGGCGGTCATTGTCACTGGTCAGCTCCAGCACCTTCTGCTGCGTC
TCCACGTTGCGCTGCTTGGCCTTGTCGCGGCTCTTGCGCACCGCGATGTTGTTGCGCTCG
CGCCGCACCCGGTACTCGTTGCTGTTCTTAGTCCACCGACTTCTTGGCCTTGCCCGCGCC
GCTGCCGCCACTCGCGCGGAGGTCGGGGTGCGCGGCGCCCAGCCCCTTGAGCGCGCTGCC
AGGGCCCGGCAGGCCGGCGGCACCGAGCGCGGGCGCGGGGTGCGGGCTGGGCACGGGCGT
GGGCGGCGGCGTGGGGTGACCGGGCTGCAGGTGCATGGTGGTCTGGCCGCAGTGCGCGAT
CTGGAACTGCAGGTGCGGGGCGGCCAGGTGCGCGGGCGGCGGGTGCGGGTGCGGGTGCGG
GTGCGAGGGCGGCGGCGGCGGCGGCGGCTGGTAAGGGAAGAGGCCGGCCAGCGCCAGCTG
CTTGGCTTCATCCTCCTCGCGGGGCTCCTGCTTGATCACCAGCGGCCGCAGCGCCGGCGC
CCCGACGCGCTCGTACAGGGGCTCCAGCCTGCCGTCCAGGTAGCCGGCGGCCGCGCAGCC
GTAGCCGGGCGGGGGCCCGTGCGCTCCCCCGGGCATGACGGCGCCGCCGGGGCCCGCGGG
CGCGCCCCGGGTAGTCAAAGTCGCCGCCGCCGCCGCCGCCCGTGGGGCCCACGGCCGCCT
TGGCCTTCTCCTGCTGCCGGCTGTGCTGGAACAGGTCGGCCAGGAACTCGTCGTTGAAGG
CGGCCGGGTCGATGTAGGCGCTGATGTCGATGGACGTCTCGTGCTCGCAGATGCCGCCCA
GCGGCTCCGGGGCGGCAGGTGGGGCGGGAGGCTGCGCGGGGCCCGCGCCCCGGGGAAAGC
CGAAGGCGGCGCTGCTGGGCGCGTGCGGGGGCTCTGCAGGTGGCTGCTCATCGGGGGCCG
CGGCTCCGCCTCGTAGAAGTCGGCCGACTCCATGGGGGAGTTAGAGTTCTCCCGGCATG

The program merges by default regions that overlap. I cannot find the way to avoid this and get one fasta read for each region of my bed.

I have been playing around with the parameters

 --interval-merging-rule,-imr <IntervalMergingRule>
                              Interval merging rule for abutting intervals  Default value: ALL. Possible values: {ALL,
                              OVERLAPPING_ONLY}

and

--interval-set-rule,-isr <IntervalSetRule>
                              Set merging approach to use for combining interval inputs  Default value: UNION. Possible
                              values: {UNION, INTERSECTION}

This is my code

gatk FastaAlternateReferenceMaker \
   -R Homo_sapiens_assembly38.fasta \
   -O output_not_merging_interval.fasta \
   -L amplicons_coo_v1.1_with_chr.bed \
   --variant Unique_indels_in_ROI_chr_sorted_left_align.vcf \