QUESTIONS in code of SV genotyping

[NMUzhoujun]

Hi,

When I was converting the cram to the fastq, I found the code in your WDL workflow:

seq 0 ~{in_nb_chunks} | head -n ~{in_max_chunks} | parallel -j ~{in_cram_convert_cores} "samtools collate -k {} -K ~{in_nb_chunks} --reference ~{in_ref_file} -Ouf ~{in_cram_file} {} | samtools fastq -1 reads.{}.R1.fastq.gz -2 reads.{}.R2.fastq.gz -0 reads.{}.o.fq.gz -s reads.{}.s.fq.gz -c 1 -N -"

However, it seems that samtools collate doesn't have the parameter "k" or "K". Could you please make an explanation for this and check which parameter was used in this step

Thanks!

[glennhickey]

This line seems to come from vg_mapgaffe_call_sv_cram.wdl:

 seq 0 ~{in_nb_chunks} | head -n ~{in_max_chunks} | parallel -j ~{in_cram_convert_cores} "samtools collate -k {} -K ~{in_nb_chunks} --reference ~{in_ref_file} -Ouf ~{in_cram_file} {} | samtools fastq -1 reads.{}.R1.fastq.gz -2 reads.{}.R2.fastq.gz -0 reads.{}.o.fq.gz -s reads.{}.s.fq.gz -c 1 -N -"
    >>>
    output {
        Array[File] output_read_chunks_1 = glob("reads.*.R1.fastq.gz")
        Array[File] output_read_chunks_2 = glob("reads.*.R2.fastq.gz")
    }
    runtime {
        cpu: in_cram_convert_cores
        memory: "50 GB"
        disks: "local-disk " + in_cram_convert_disk + " SSD"
        docker: "jmonlong/samtools-jm:release-1.19jm0.2.2"
        preemptible: in_preemptible
    }

Which specifies this image: docker: "jmonlong/samtools-jm:release-1.19jm0.2.2". And the collate in there has -k

docker run jmonlong/samtools-jm:release-1.19jm0.2.2 samtools collate
Usage: samtools collate [-Ou] [-o <name>] [-n nFiles] [-l cLevel] <in.bam> [<prefix>]

Options:
      -O       output to stdout
      -o       output file name (use prefix if not set)
      -u       uncompressed BAM output
      -f       fast (only primary alignments)
      -r       working reads stored (with -f) [10000]
      -l INT   compression level [1]
      -n INT   number of temporary files [64]
      -k INT   the read chunk to output during CRAM conversion. In [0,N-1]. Used if N>0.
      -K INT   the number of read chunks to consider during CRAM conversion. 0 (default) means no chunking.
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
      --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]
  <prefix> is required unless the -o or -O options are used.

This is a customized samtools: https://github.com/jmonlong/samtools-jm

[NMUzhoujun]

Thank you. It has been solved