基因数据处理50之cs-bwamem、bwa、snap、bwa-mem与art比较
发布时间：2021-03-12 09:14:30 所属栏目：大数据 来源：网络整理
导读：直接看结果： （1）art仿真数据： hadoop @Master :~/cloud/adam/xubo/data/GRCH38Sub/cs-bwamem $ cat G38L100c50Nhs20 .aln ##ART_Illumina read_length 100 @CM art_illumina -ss HS20 -i GRCH38chr1L3556522 .fna -l 100 -c 50 -o G38L100c50Nhs20 -rs 1
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(4)cs-bwamem： +--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+ | contig| start| end|mapq|readName| sequence| qual|cigar|basesTrimmedFromStart|basesTrimmedFromEnd|readPaired|properPair|readMapped|mateMapped|firstOfPair|secondOfPair|failedVendorQualityChecks|duplicateRead|readNegativeStrand|mateNegativeStrand|primaryAlignment|secondaryAlignment|supplementaryAlignment|mismatchingPositions|origQual| attributes|recordGroupName|recordGroupSequencingCenter|recordGroupDescription|recordGroupRunDateEpoch|recordGroupFlowOrder|recordGroupKeySequence|recordGroupLibrary|recordGroupPredictedMedianInsertSize|recordGroupPlatform|recordGroupPlatformUnit|recordGroupSample|mateAlignmentStart|mateAlignmentEnd|mateContig| +--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+ |[chr1,248956422,n...| 93465784| 93465884| 26| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| true| false| false| 100| null|NM:i:0 AS:i:100 X...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...|101668921|101669021| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...|231780491|231780591| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,D8...| 100M| 0| 0| false| false| true| false| false| false| false| false| true| false| false| true| false| 80C9C9| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...| 69447775| 69447875| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...| 71519060| 71519160| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|187344346|187344446| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...|188353053|188353153| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|242097330|242097430| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...|112217125|112217225| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|218009808|218009908| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...|147407851|147407951| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...| 45962351| 45962451| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...| 47126825| 47126925| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|152431792|152431892| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...|237080611|237080711| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...| 82131491| 82131591| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...| 69486875| 69486975| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...|224551051|224551151| 0| chr1-50|TTAAAAAGTCAGGAAAC...|DCDDE<DFEC<CCD,n...|154119974|154120074| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| |[chr1,n...| 78244128| 78244228| 0| chr1-50|TTCCACAATAGTTGAAC...|@@CDFDFDHFHGHIJH:...| 100M| 0| 0| false| false| true| false| false| false| false| false| false| false| false| true| false| 9G9G80| null|NM:i:2 AS:i:90 RG...| foo| null| null| null| null| null| null| null| null| null| bar| null| null| null| +--------------------+---------+---------+----+--------+--------------------+--------------------+-----+---------------------+-------------------+----------+----------+----------+----------+-----------+------------+-------------------------+-------------+------------------+------------------+----------------+------------------+----------------------+--------------------+--------+--------------------+---------------+---------------------------+----------------------+-----------------------+--------------------+----------------------+------------------+------------------------------------+-------------------+-----------------------+-----------------+------------------+----------------+----------+ only showing top 20 rows 492条 （编辑：晋中站长网） 【声明】本站内容均来自网络，其相关言论仅代表作者个人观点，不代表本站立场。若无意侵犯到您的权利，请及时与联系站长删除相关内容! |
