SAMPLE=HG002
THR=48

biastools --analyze --real -t $THR -o ${SAMPLE}_plot -g ~/data_blangme2/fasta/grch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
          -v ${SAMPLE}_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -s ${SAMPLE} -r edit_imputefirst-leviosam \
          --bam /vast/blangme2/smajidi5/impute-first/abra_leviosam/${SAMPLE}.BBBC20/${SAMPLE}.BBBC20_HGSVC3.L50.chm13.L50.g70.bam_abra.bam 

biastools --analyze --real -t $THR -o ${SAMPLE}_plot -g ~/data_blangme2/fasta/grch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
          -v ${SAMPLE}_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -s ${SAMPLE} -r edit_imputefirst-giraffe \
          --bam /vast/blangme2/smajidi5/impute-first/abra_giraffeimputefirst/HG2_sorted2_bbbc20/HG2_sorted2_bbbc20_rg.bam_abra.bam 

biastools --analyze --real -t $THR -o ${SAMPLE}_plot -g ~/data_blangme2/fasta/grch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
          -v ${SAMPLE}_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -s ${SAMPLE} -r edit_VG_personalized \
          --bam /vast/blangme2/smajidi5/impute-first/vg_graph/t10_${SAMPLE}/aligned_38_sorted_abra.bam 

biastools --analyze --real -t $THR -o ${SAMPLE}_plot -g ~/data_blangme2/fasta/grch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
          -v ${SAMPLE}_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -s ${SAMPLE} -r edit_linear_bwa \
          --bam ~/vast/personalized_leviosam/${SAMPLE}_bams/bwa_linear.bam 

biastools --analyze --real -t $THR -o ${SAMPLE}_plot -g ~/data_blangme2/fasta/grch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
          -v ${SAMPLE}_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -s ${SAMPLE} -r edit_pangenome_1kgp \
          --bam ~/vast/personalized_leviosam/${SAMPLE}_bams/1kgp_pangenome_rg.bam 

biastools --analyze --real -t $THR -o ${SAMPLE}_plot -g ~/data_blangme2/fasta/grch38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
          -v ${SAMPLE}_GRCh38_1_22_v4.2.1_benchmark.vcf.gz -s ${SAMPLE} -r edit_pangenome_hprc \
          --bam ${SAMPLE}_sorted2_HPRC_rg.bam 
