What does this mean
XP:Z:1,+150884058,55M45S,0,0;
This is the entire read
HS2000-645_410:4:2313:12585:49651 353 22 37097777 0 54S46M = 37097858 181 GCCATCACACCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTACACAAATACACACACGCAGCCAGCCACCTCGAGTGATATGTGTG <=<ABBCABA@AB@@A@@@@?@;A<?@?@@@@A=?@@A@>9A=:21,/5=?1@.29@A@A@@<A@A@A@B?=:;B+&;=>BBB/=7=?C==DCDCDB@AA BD:Z:JJNMPPOKJJNMNMNMKJJJCCCKHKHJCCCJLLKLJKJLJJIILJCJKHLLKLHKKHHHIBJHKHHIIIIKMNNONMNONMJNNLMMNOKPOLMQIIII PG:Z:MarkDuplicates RG:Z:XXXXXXXXXX(sample id) BI:Z:LLONPPQLLKOOPNPPNLLKFFFNKNKKFFFMONNOLMLMMLKKOLGLOKONNNLONKKKMFMKNKKKKKKOOQQRPOQRPOMQQNNQQRPTSPQSLLLL NM:i:0 XP:Z:1,+150884058,55M45S,0,0; MQ:i:60 AS:i:46 XS:i:20
Is there a bitwise flag to were I can view reads with only this XP? Similar to samtools view in.bam | grep "XP:" but without the grep so I can do samtools view -f ??? -c in.bam and return the counts.
Super-duper thanks.
•
written
by
QVINTVS_FABIVS_MAXIMVS
XP is an old tag and has been renamed SA in the sam spec:
http://samtools.github.io/hts-specs/SAMv1.pdf
Other canonical alignments in a chimeric alignment, formatted as a semicolon-delimited list:
{\tt (}\emph{rname}{\tt ,}\emph{pos}{\tt ,}\emph{strand}{\tt ,}\emph{CIGAR}{\tt ,}\emph{mapQ}{\tt ,}\emph{NM}{\tt ;)}+.
Each element in the list represents a part of the chimeric alignment. Conventionally, at a supplementary line,
the first element points to the primary line.\\
Thanks, is there a bitwise flag I can use to find all the reads?
$ samtools view -f ??? in.bam 1:1000-2000
Using my tool samjs
java -jar dist-1.133/samjs.jar -e 'record.getAttribute("SA")!=null' input.bam
What tool are you using to generate these BAM files? According to the bam spec, tags that start with X are reserved for local use. Maybe there are hints on what the field means in the header (type in samtools view -H file.bam)
BWA-MEM with split read option on
ID:GATK IndelRealigner VN:2.5-2-gf57256b CL:knownAlleles=[(RodBinding name=knownAlleles source=/----/----/----/temp_project/broad_bundles/2.3/b37/Mills_and_1000G_gold_standard.indels.b37.vcf)] targetIntervals=/----/---/----/----/----/----/----/---- LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null
@PG ID:MarkDuplicates PN:MarkDuplicates VN:1.86(1363) CL:net.sf.picard.sam.MarkDuplicates INPUT=[/----/----/----/-----/----/----/----/----] OUTPUT=/----/----/----/----/----/----/----/---- METRICS_FILE=/----/ REMOVE_DUPLICATES=true ASSUME_SORTED=true MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
@PG ID:GATK PrintReads VN:2.5-2-gf57256b CL:readGroup=null platform=null number=-1 downsample_coverage=1.0 sample_file=[] sample_name=[] simplify=false no_pg_tag=false
@CO Sorting ----.bam file with piacrd tool
Log in to answer this question.
As I said in the other thread, update to the latest version of bwa.