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../output/02.10-bismark-deduplication/CF05-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF05-CM05-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF06-CM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF06-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF07-CM02-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF08-CM03-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF08-CM04-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF08-CM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF01-EM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF02-EM02-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF03-EM03-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF03-EM04-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF03-EM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF04-EM04-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF04-EM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF05-EM01-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF05-EM05-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF05-EM06-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF06-EM01-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF06-EM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF06-EM06-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF07-EM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF07-EM03-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF08-EM03-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF08-EM04-Larvae_dedup.sorted.bam @PG ID:samtools.10 PN:samtools PP:samtools.5-3AF18A0 VN:1.19.2 CL:samtools merge --threads 20 -o ../output/12-snp-calling-BS-Snper/merged_offspring_threads_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF01-CM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF01-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF02-CM02-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF03-CM03-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF03-CM04-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF03-CM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF04-CM04-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF05-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF05-CM05-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF06-CM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF06-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF07-CM02-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF08-CM03-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF08-CM04-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF08-CM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF01-EM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF02-EM02-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF03-EM03-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF03-EM04-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF03-EM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF04-EM04-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF04-EM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF05-EM01-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF05-EM05-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF05-EM06-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF06-EM01-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF06-EM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF06-EM06-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF07-EM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF07-EM03-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF08-EM03-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/EF08-EM04-Larvae_dedup.sorted.bam @PG ID:samtools.11 PN:samtools PP:samtools.5-C483E42 VN:1.19.2 CL:samtools merge --threads 20 -o ../output/12-snp-calling-BS-Snper/merged_offspring_threads_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF01-CM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF01-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF02-CM02-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF03-CM03-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF03-CM04-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF03-CM05-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF04-CM04-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF05-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF05-CM05-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF06-CM01-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF06-CM02-Larvae_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF07-CM02-Zygote_dedup.sorted.bam ../output/02.10-bismark-deduplication/CF08-CM03-Zygote_dedup.sorted.bam ../output/02.10-bismark-dedupl