[{"_1":2,"_188":-5,"_189":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_163":164},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":85,"_106":107,"_154":-5,"_155":11,"_156":17,"_157":11,"_158":-5,"_159":11,"_160":-5,"_161":162},"canonicalUrl","https://hub.docker.com/r/statgen/alignment/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","statgen","reponame","alignment","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":70,"_75":17,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2016-08-19T19:38:27.10415Z","description","Alignment","is_private","last_updated","2018-06-21T21:19:56.199533Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",277386,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# docker-alignment\nDocker image for alignment.\n\n## Pre-align\n```bash\nsamtools view -uh -F 0x900 $local_input_file \\\n | bam-ext-mem-sort-manager squeeze --in -.ubam --keepDups --rmTags AS:i,BD:Z,BI:Z,XS:i,MC:Z,MD:Z,NM:i,MQ:i --out -.ubam \\\n | samtools sort -l 1 -@ 1 -n -T .samtools_sort_tmp - \\\n | samtools fixmate - - \\\n | bam-ext-mem-sort-manager bam2fastq --in -.bam --outBase --maxRecordLimitPerFq 20000000 --sortByReadNameOnTheFly --readname --gzip\n```\n\n\n## Align\n```bash\nref_path=\npre_output_base=\n\nwhile read line\ndo\n line_rg=$(echo $line | cut -d ' ' -f 4- | sed -e \"s/ /\\\\\\t/g\")\n input_path=$(echo $line | cut -f 2 -d ' ')\n input_filename=$(basename $input_path)\n output_filename=$(basename $input_filename \".fastq.gz\").cram\n\n paired_flag=\"\"\n if [[ $input_file_name =~ interleaved\\.fastq\\.gz$ ]]\n then\n paired_flag=\"-p\"\n fi\n\n bwa mem -t 32 -K 100000000 -Y ${paired_flag} -R \"$line_rg\" $ref_path $input_path | samblaster -a --addMateTags | samtools view -@ 32 -T $ref_path -C -o $output_filename - \ndone <<< \"$(tail -n +2 ${pre_output_base}.list)\"\n```\n\n## Post-align\n```bash\ninput_dir=\nref_path=\ndbsnp_path=\nrc=0\nfor input_file in ${input_dir}/*.cram \ndo \n tmp_prefix=${input_file%.cram}.tmp\n samtools sort --reference /home/alignment/ref/hs38DH.fa --threads 1 -T $tmp_prefix -o ${input_file%.cram}.sorted.bam $input_file\n rc=$?\n [[ $rc != 0 ]] && break\n rm -f $input_file ${tmp_prefix}*\ndone\n\nif [[ $rc == 0 ]]\nthen \n samtools merge --threads 1 -c ${input_dir}/merged.bam ${input_dir}/*.sorted.bam \\\n && rm ${input_dir}/*.sorted.bam \\\n && bam-non-primary-dedup dedup_LowMem --allReadNames --binCustom --binQualS 0:2,3:3,4:4,5:5,6:6,7:10,13:20,23:30 --log ${input_dir}/dedup_lowmem.metrics --recab --in ${input_dir}/merged.bam --out -.ubam --refFile $ref_path --dbsnp $dbsnp_path \\\n | samtools view -h -C -T ${ref_path} -o ${input_dir}/output.cram --threads 1\n rc=$?\nfi\n```","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",2052522272,"orgData",{"_86":87,"_88":89,"_90":91,"_92":29,"_93":94,"_95":96,"_97":98,"_99":94,"_100":101,"_102":94,"_103":94,"_104":94,"_105":17},"id","52f02499e2fc44b6911b9a2679655699","uuid","52f02499-e2fc-44b6-911b-9a2679655699","type","organization","orgname","full_name","","location","Ann Arbor, MI","company","University of Michigan School of Public Health","profile_url","date_joined","2016-07-01T20:03:32.706644Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[108,144],{"_109":40,"_110":111,"_112":113,"_86":114,"_115":116,"_46":133,"_134":111,"_135":29,"_136":52,"_53":137,"_138":139,"_140":124,"_141":133,"_142":62,"_143":17},"content_type","creator",944982,"full_size",249855659,4418150,"images",[117],{"_118":119,"_120":121,"_122":94,"_123":124,"_125":126,"_127":128,"_129":94,"_130":-5,"_131":113,"_59":62,"_132":-5},"architecture","amd64","digest","sha256:054920a3bae8916d37a62dfbb92a70e64a22f29b1555f656fb9ad6216ef6a6a9","features","last_pulled","2026-09-22T08:29:42.509593749Z","last_pushed","2018-06-21T21:06:52Z","os","linux","os_features","os_version","size","variant","2018-06-21T21:06:51.528955Z","last_updater","last_updater_username","media_type","latest","repository",867205,"tag_last_pulled","tag_last_pushed","tag_status","v2",{"_109":40,"_110":111,"_112":145,"_86":146,"_115":147,"_46":152,"_134":111,"_135":29,"_136":52,"_53":153,"_138":139,"_140":150,"_141":152,"_142":62,"_143":17},249855834,29649299,[148],{"_118":119,"_120":149,"_122":94,"_123":150,"_125":151,"_127":128,"_129":94,"_130":-5,"_131":145,"_59":62,"_132":-5},"sha256:662b3456a3c227e4838b5e4142651bdf3e31d4e9e1afa62246f11769f51caf1d","2026-09-20T17:11:24.496564728Z","2018-06-21T21:19:56Z","2018-06-21T21:19:55.934411Z","1.0.0","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":165,"_172":173,"_161":186,"_187":11},{"_36":166,"_38":167,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":168,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":169,"_75":17,"_76":171,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":170},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_174":175,"_176":-5,"_177":-5,"_178":179},"count",2,"next","previous","results",[180,183],{"_109":40,"_110":111,"_112":145,"_86":146,"_115":181,"_46":152,"_134":111,"_135":29,"_136":52,"_53":153,"_138":139,"_140":150,"_141":152,"_142":62,"_143":17},[182],{"_118":119,"_120":149,"_122":94,"_123":150,"_125":151,"_127":128,"_129":94,"_130":-5,"_131":145,"_59":62,"_132":-5},{"_109":40,"_110":111,"_112":113,"_86":114,"_115":184,"_46":133,"_134":111,"_135":29,"_136":52,"_53":137,"_138":139,"_140":124,"_141":133,"_142":62,"_143":17},[185],{"_118":119,"_120":121,"_122":94,"_123":124,"_125":126,"_127":128,"_129":94,"_130":-5,"_131":113,"_59":62,"_132":-5},[],"canDeleteTags","actionData","errors"]

statgen/alignment

Tags for statgen/alignment