For each alignment, optionally write it in a FASTQ file (or a pair of) if the MAPQ of it is below a given cutoff. If this option gets activated, don't write low-MAPQ alignments to the lifted BAM output.

Hello,
The documentation does not list the SA flag as lifted, and from reading the code I think that it is indeed not the case. Could you confirm this?
Is this a development you are considering? I guess the logic would be fairly similar to ChainMap::lift_segment, would it not?
Thanks and best regards,
Daniel Naro

Feature request

Switch to the bcftools v1.11 (especially for bcftools consensus) logic in levioSAM serialize when dealing with overlapping variants. LevioSAM is developed base on some logic between bcftools v1.9 and v1.10, but sadly it is no longer the official logic right now.

An example

$bcftools view -H wg-maj.vcf.gz chr20:5099236-5099250
chr20	5099236	.	C	A
chr20	5099236	.	CAATCAATCAATA	C
chr20	5099240	.	C	A
chr20	5099244	.	C	A

Using bcftools v1.11

$samtools faidx wg-maj.chr20.v1_11.fa chr20:5099100-5099500
>chr20:5099100-5099500
TGTCTCAAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAATAAATAA
AAAAACCAAATCATTTGGTTGGCCAAAACCTTCTGATCTGAGCTTTGCTCGGCAACCACT
CTCCAAGATAAAGCTTTATGTATCACCTCACATATTCACTGTCAAGGCTCAGGCACTCTA
GATTACTGGACTCCCCAGTCAACATTCCCATTACCAAAAGTCCCTAATCTTGGAGGCTGC
TTCAGGTCACCCTCTCTTTGTCCCTCACTTCCTGAGTTTTTTTTTTTTCCTCCAACTATA
CTCACTCTACTGGTGATCTCAAACAGCCCTCTAGCTTTTAAGATACTGTCCAAATGCTGA
CTCCCAAATTTCTATTTCCATCCAAGACCCACTCTTAAACT

Using bcftools v1.9-206-g4694164

The 11-bp deletion (CAATCAATCAATA>C) is not updated here.

$samtools faidx wg-maj.chr20.v1_9_206_g4694164.fa chr20:5099100-5099500
>chr20:5099100-5099500
TGTCTCAAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATA
AATAATAAATAAAAAAACCAAATCATTTGGTTGGCCAAAACCTTCTGATCTGAGCTTTGC
TCGGCAACCACTCTCCAAGATAAAGCTTTATGTATCACCTCACATATTCACTGTCAAGGC
TCAGGCACTCTAGATTACTGGACTCCCCAGTCAACATTCCCATTACCAAAAGTCCCTAAT
CTTGGAGGCTGCTTCAGGTCACCCTCTCTTTGTCCCTCACTTCCTGAGTTTTTTTTTTTT
CCTCCAACTATACTCACTCTACTGGTGATCTCAAACAGCCCTCTAGCTTTTAAGATACTG
TCCAAATGCTGACTCCCAAATTTCTATTTCCATCCAAGACC

This includes changing CIGAR and trimming corresponding SEQ and QUAL bases.

Hello! Reading the documentation, it didn't seem like there was anything written about the use of phased vs. unphased VCFs. Is levioSAM capable of taking in unphased VCFs to perform lift overs?