fastq

Category: ALIGNMENT

Convert BAM to FASTQ format

Description

Convert a BAM file to interleaved FASTQ format.

Reads BAM records and outputs FASTQ to stdout for piping to aligners. Input should be queryname-sorted or template-coordinate sorted.

EXAMPLES:

fgumi fastq -i unmapped.bam | bwa mem -t 16 -p -K 150000000 -Y ref.fa -

fgumi fastq -i unmapped.bam -@ 4 | bwa mem -t 16 -p ref.fa -

fgumi fastq -i aligned.bam -F 0x900 | bwa mem …

Flag	Description	Default
`-i, --input <INPUT>`	Input BAM file	required
`-o, --output <OUTPUT>`	Output FASTQ file. If omitted, the FASTQ stream is written to stdout (the default, intended for piping straight to an aligner)
`-n, --no-read-suffix <NO_SUFFIX>`	Don’t append /1 and /2 to read names	`false`
`-F, --exclude-flags <EXCLUDE_FLAGS>`	Exclude reads with any of these flags present [0x900 = secondary\|supplementary]	`2304`
`-f, --require-flags <REQUIRE_FLAGS>`	Only include reads with all of these flags present	`0`
`-@, --threads <THREADS>`	Number of threads for BAM decompression	`1`
`-K, --bwa-chunk-size <BWA_CHUNK_SIZE>`	BWA -K parameter value (bases per batch). Sizes output buffer to match bwa’s batch size for optimal pipe throughput. Default matches common bwa mem usage	`150000000`