<?xml version="1.0" encoding="UTF-8"?>
<RUN_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <RUN alias="970678a55d6d0f17d6e55e88fda079ce" center_name="Illumina Fast Track Services" broker_name="UM-SPH" run_center="Illumina Fast Track Services" accession="SRR5145359">
    <IDENTIFIERS>
      <PRIMARY_ID>SRR5145359</PRIMARY_ID>
      <SUBMITTER_ID namespace="Illumina Fast Track Services">970678a55d6d0f17d6e55e88fda079ce</SUBMITTER_ID>
    </IDENTIFIERS>
    <TITLE>Secondary mapping Build 37 for NWD100505 [2830]</TITLE>
    <EXPERIMENT_REF accession="SRX2455543" refname="NWD100505-expt" refcenter="Illumina Fast Track Services"/>
    <PROCESSING>
      <PIPELINE>
        <PIPE_SECTION section_name="read mapping">
          <STEP_INDEX> none </STEP_INDEX>
          <PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
          <PROGRAM> iSAAC </PROGRAM>
          <VERSION> iSAAC-01.14.02.06 </VERSION>
          <NOTES> genome reference sequence UCSC hg19 without decoy sequences </NOTES>
        </PIPE_SECTION>
        <PIPE_SECTION section_name="sort / merge / mark duplicates / realign around indels">
          <STEP_INDEX> new </STEP_INDEX>
          <PREV_STEP_INDEX> none </PREV_STEP_INDEX>
          <PROGRAM> iSAAC </PROGRAM>
          <VERSION> iSAAC-01.14.02.06 </VERSION>
          <NOTES/>
        </PIPE_SECTION>
        <PIPE_SECTION section_name="convert to .cram format">
          <STEP_INDEX> home </STEP_INDEX>
          <PREV_STEP_INDEX> new </PREV_STEP_INDEX>
          <PROGRAM> samtools view -C </PROGRAM>
          <VERSION> 1.3.1 Using htslib 1.3.1 </VERSION>
          <NOTES> genome reference sequence retrieved from:    ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz   with UCSC's choice of human mitochondrial sequence NC_001807.4, gi 17981852 of length 16,571   replacing the revised Cambridge reference sequence NC_012920, gi 251831106 of length 16,569 </NOTES>
        </PIPE_SECTION>
      </PIPELINE>
    </PROCESSING>
    <RUN_ATTRIBUTES>
      <RUN_ATTRIBUTE>
        <TAG>assembly</TAG>
        <VALUE>GRCh37</VALUE>
      </RUN_ATTRIBUTE>
      <RUN_ATTRIBUTE>
        <TAG>Alignment Provider</TAG>
        <VALUE>Sequencing Center</VALUE>
      </RUN_ATTRIBUTE>
    </RUN_ATTRIBUTES>
  </RUN>
</RUN_SET>
