<NON_REF> in .vcf.gz ALT column

[Yegor Korovin]

Hallo,

I have some issues with output of elprep. I'm running elprep as follows:

elprep filter input/NA12877_GCA_mapped.bam NA12877_GCA_mapped.elprep.output.bam \
        --mark-duplicates --mark-optical-duplicates NA12877_GCA.output.metrics \
        --sorting-order coordinate \
        --bqsr NA12877_GCA.output.recal \
        --known-sites resources/Homo_sapiens_assembly38.dbsnp138.elsites,resources/Mills_and_1000G_gold_standard.indels.hg38.elsites \
        --reference resources/hg38.elfasta \
        --haplotypecaller NA12877_GCA.vcf.gz

The problem is that inside the vcf file all of the 'ALT' column is filled with <NON_REF> and the QUAL is absent. Here is a sample line from vcf:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample1

chr1    10353   .       A       <NON_REF>       .       .       END=10358       GT:DP:GQ:MIN_DP:PL      0/0:1:3:1:0,3,35

...

In log files there is nothing catching my eye. The same happens in sfm mode. Do you have an idea, what am I doing wrong?

And another, unrelated, question. As far as I understand, GATK recommends performing SortAndFixTags after marking duplicates and before BQSR  What is the status of this step? Is it really recommended? I see that sample elprep command omits this step. Or is it possible to incorporate it in elprep as well?

With the best wishes,

Yegor