How_to_get_bam_and_vcf.md

To generate BAM file for the target region:

step1. generate the bed file "selected.bed".

The bed file contains the chromosome name, start position and end position of your target region. eg. chr1 123456 223456.

step2. generate the "selected.bam" by a WGS bam file (or a bam file from one specific chromosome) and the bed file.

samtools -b -L selected.bed wgs.bam > selected.bam

samtools index selected.bam

To generate the original WGS bam file for 10X or stLFR linked-reads, you can run LongRanger/EMA/BWA. Check here for more details.

To generate VCF file through FreeBayes:

freebayes -f genome_hg19.fa wgs.bam > test_freebayes.vcf

or

freebayes -f genome_hg19.fa selected.bam > test_freebayes.vcf

Once you generate the selected.bam and test_freebayes.vcf in your working directory, you can use use it to run AquilaSV pipeline.