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Compression - Quick Guide
Compressing FASTQ
Compressing BAM
Compressing VCF
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Analyzing data
Genozip includes a number of analysis tools:
Summary statistics
Coverage and Depth (BAM and FASTQ)
Sex Classification (BAM and FASTQ)
idxstats (BAM and FASTQ)
Compression Performance
Filtering & subsetting
Subsetting command line options
Filtering by species using kraken2 (BAM / FASTQ)
Downsampling and Sharding
Format conversions
Dual-Coordinate VCF
Converting BAM/SAM to FASTQ
Converting 23andMe to VCF
Converting MultiFASTA to PHYLIP and back
Miscellaneous
FASTQ-to-BAM pipeline using Genozip
Fixing Contig Names (eg chr22 ⇆ 22)
Handling GATK's "Unexpected base in allele bases"
Genozip diagnostics (for technical support)
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