Exomedepth:

$ awk -F"__" '$1=$1' OFS="\t" PAHC44_1_CDHS-17427Z-2274_sorted.bed | cut -f1,2,3,4 > qiaseq_PAHC44_1_CDHS-17427Z-2274_no_header.bed


DeviCNV:

$ echo -e "Amplicon_ID\tChr\tAmplicon_Start\tAmplicon_End\tInsert_Start\tInsert_End\tGene\tTranscript\tExon\tPool" > qiaseq_PAHC44_1_CDHS-17427Z-2274_no_header.devicnv.bed
$ awk -F"__" '$1=$1' OFS="\t" PAHC44_1_CDHS-17427Z-2274_sorted.bed | awk '{ print $4"."$7"\t"$1"\t"$2"\t"$3"\t"$2"\t"$3"\t"$4"\t"$4"\t"$7"\t"Pool1}' >> qiaseq_PAHC44_1_CDHS-17427Z-2274_no_header.devicnv.bed