bwa mem in sarek does not align to ALT chromosomes

[mggrami]

why is that? What command is the cause of such behavior? Are those positions somehow compensated in further analysis to prevent false discoveries of snps?

Sincerely,

Michał

[FriederikeHanssen]

Ae the ALT chromosomes part of your index?

[mggrami]

Yes! I am using --genome GATK.GRCh38

[mggrami]

nextflow run nf-core/sarek -profile docker --input samplesheet_T1.csv --outdir results_INEZ_07_03_25_T1/ --genome GATK.GRCh38 --intervals /media/mg/iccvs/S07604514_hg38/nohead_Covered.bed --wes --tools haplotypecaller,manta,mutect2,snpeff --trim_fastq TRUE --save_mapped --save_output_as_bam --max_memory 120GB --max_cpus 30

This is the command