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Y chromosome SNPs not found in YCC and cannot be assigned to a particular haplogroup
I've been doing ancient DNA analysis in Egyptian mummies and I have some issues with my Y chromosome SNPs.
First of all when I map my dataset to the hg19 I have less SNPs than when I map it only to the Y-chromosome and also different ones. I do the SNP calling with GATK in which case I have very few haplotypes, and also I call SNPs from Geneious in which case I have way more. The common ones between GATK and Geneious are less than 10.
My biggest problem is that when I search the UCSC genome browser they come up as validated with an rs number and all, but I cannot find them in the YCC publication, therefore I cannot assign them in a particular haplogroup which is what I have to get out of this analysis. Below are the commands that I'm running to call SNPs after the local realignment and recalibration. Any help would be very much appreciated.
java -jar ../../../NGS_programs/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T HaplotypeCaller -R ../../GRCh38_hg38_WholeGenomewithrepeats/hg38.fa -I ../../../NGS_Data/NA_chromosomeY_NGS/NA_Y_mapped_to_complete_genome_GRC38_hg38/NA_Y_TTCTTGAC-GCGCGTAG.hg38aligned.MERGED.Groups.Added.indelrealigner.recal.bam -o NA_Y_TTCTTGAC-GCGCGTAG.hg38aligned.MERGED.HaplotypeCaller.vcf
java -jar ../../../NGS_programs/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T SelectVariants -R ../../
GRCh38_hg38_WholeGGRCh38_hg38_WholeGenomewithrepeats/hg38.fa -V NA_Y_TTCTTGAC-GCGCGTAG.hg38aligned.MERGED.HaplotypeCallertest.vcf -selectType SNP -o NA_Y_TTCTTGAC-GCGCGTAG.hg38aligned.MERGED.SelectVariants.vcf
java -jar ../../../NGS_programs/GenomeAnalysisTK-3.5/GenomeAnalysisTK.jar -T VariantFiltration -R ../../GRCh38_hg38_WholeGenomewithrepeats/hg38.fa -V NA_Y_TTCTTGAC-GCGCGTAG.hg38aligned.MERGED.SelectVariants.vcf --filterExpression "DP < 5" --filterName "NA_Y_filter_GATK" -o NA_Y_GATK_filtered_snps_VariantFiltration.vcf
The last command I have also tried with default values i.e. --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" --filterName "NA_Y_filter_GATK" but nothing changed.
Thank you all.