Strange symbols in "ALT" field

[enabieva]

Hi (Thank you for answering my other question).
cctools genotype writes strange symbols into the vcf file.
An example bam, index and output files can be found at https://cb.skoltech.ru/~enabieva/for_cleancall/ (the browser may complain about the certificate). An example of an offending line is on line 80 (chr20:310376). The reference is ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa
The vcf file is the HapMap3.3 from the GATK Resource Bundle (ftp://[email protected]/bundle/hg38/hapmap_3.3.hg38.vcf.gz)

Another issue I'm having is that if I don't restrict genotype to a particular chromosome, (chr20 in the example), it creates a Makefile target that's called just ".tbi" and then complains about it. I think it might have to do with prefixing the chromosome name with "chr".

[enabieva]

These symbols appear in areas where the input bams have no coverage.