What does this mean in my read (samtools)
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9.1 years ago

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.

ngs samtools wgs • 2.8k views
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As I said in the other thread, update to the latest version of bwa.

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9.1 years ago

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.\\
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Thanks, is there a bitwise flag I can use to find all the reads?

$ samtools view -f ??? in.bam 1:1000-2000
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Using my tool samjs

java -jar dist-1.133/samjs.jar -e 'record.getAttribute("SA")!=null' input.bam
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9.1 years ago
Ying W ★ 4.3k

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)

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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
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