jvarkit
Biostar352930
Fills the empty SEQ() and QUAL() in a bam file using the the reads with the same name carrying this information.
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar biostar352930 [options] Files
Usage: biostar352930 [options] Files
Options:
--bamcompression
Compression Level. 0: no compression. 9: max compression;
Default: 5
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--version
print version and exit
Keywords
- sam
- bam
See also in Biostars
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite biostar352930 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Motivation
Fills the empty SEQ() and QUAL() in a bam file using the the reads with the same name carrying this information.
Input
a sam or a bam file. Input MUST be sorted on query name using picard. ( see see https://github.com/samtools/hts-specs/issues/5 )
Example
A read A00223:8:H7YG3DMXX:1:1101:1163:35383 in the remote bam file below is missing SEQ/QUAL while another has this information
$ wget -q -O - "https://gist.githubusercontent.com/toddknutson/90430a0dd736898037ed18bcd044df7f/raw/87c1ea5a548ac71c628d2b72f5bd6ee6415efbcd/gistfile1.txt" | grep -F "A00223:8:H7YG3DMXX:1:1101:1163:35383"
A00223:8:H7YG3DMXX:1:1101:1163:35383 16 chr7 6027025 9 151M * 0 0 GCTAGAAGACAGCAGACCCCTTGTCTGTCCTAGAGGGCTCCTTCTTGGTTCTGGAGTCTTTGGGCTGTGAGGCTTGTTCTCTGTTGTGTGACGAAGAGAAAAGGCCTCTCGCAGTCTGGAAATGGACACGTCTTTTTTTTCTTCTCCAGTC FFFFFFFFFFFFFF,:FFFF,F,FFFFFFFF:FFFFFFFFF:FF::FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFF NM:i:2 MD:Z:14T7T128 AS:i:2978 XS:i:2894 RG:Z:INV_4SMALL_Aug_17_2017_1
A00223:8:H7YG3DMXX:1:1101:1163:35383 256 chr7 6776783 0 151M * 0 0 * * NM:i:6 MD:Z:17G0G109A7A2T0C10 AS:i:2894 RG:Z:INV_4SMALL_Aug_17_2017_1
get the sam/bam file, sort it on queryname using picard
$ wget -q -O - "https://gist.githubusercontent.com/toddknutson/90430a0dd736898037ed18bcd044df7f/raw/87c1ea5a548ac71c628d2b72f5bd6ee6415efbcd/gistfile1.txt" |\
java -jar /path/to/picard.jar SortSam I=/dev/stdin O=/dev/stdout SO=queryname VALIDATION_STRINGENCY=LENIENT |\
java -jar dist/biostar352930.jar
output:
@HD VN:1.5 SO:queryname
(...)
@RG ID:INV_4SMALL_Aug_17_2017_1 SM:0X PL:ILLUMINA LB:libeX
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem -t 12 -R @RG\tID:sample1\tSM:0X\tPL:ILLUMINA\tLB:libeX -Y -a -k 11 -O 2 -B 1 -A 20 hg19_canonical_PARmaskedonchrY.fasta R1.fastq
@CO biostar352930. compilation: 2018-12-05:10-12-50 githash: 03f79caf6a62458937b2d55d0661737617334733 htsjdk: 2.15.0. cmd:
A00223:8:H7YG3DMXX:1:1101:1163:35383 256 chr7 6776783 0 151M * 0 0 GACTGGAGAAGAAAAAAAAGACGTGTCCATTTCCAGACTGCGAGAGGCCTTTTCTCTTCGTCACACAACAGAGAACAAGCCTCACAGCCCAAAGACTCCAGAACCAAGAAGGAGCCCTCTAGGACAGACAAGGGGTCTGCTGTCTTCTAGC FFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF::FF:FFFFFFFFF:FFFFFFFF,F,FFFF:,FFFFFFFFFFFFFF MD:Z:17G0G109A7A2T0C10 RG:Z:INV_4SMALL_Aug_17_2017_1 NM:i:6 AS:i:2894
A00223:8:H7YG3DMXX:1:1101:1163:35383 16 chr7 6027025 9 151M * 0 0 GCTAGAAGACAGCAGACCCCTTGTCTGTCCTAGAGGGCTCCTTCTTGGTTCTGGAGTCTTTGGGCTGTGAGGCTTGTTCTCTGTTGTGTGACGAAGAGAAAAGGCCTCTCGCAGTCTGGAAATGGACACGTCTTTTTTTTCTTCTCCAGTC FFFFFFFFFFFFFF,:FFFF,F,FFFFFFFF:FFFFFFFFF:FF::FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFF MD:Z:14T7T128 RG:Z:INV_4SMALL_Aug_17_2017_1 NM:i:2 AS:i:2978 XS:i:2894
A00223:8:H7YG3DMXX:1:1101:15338:10113 256 chr7 6777077 0 151M * 0 0 GTTCAGCATCCCAGACACGGGCAGTCACTGCAGCAGCGAGTATGCGGCCAGCTCCCCAGGGGACAGGGGCTCGCAGGAACATGTGGACTCTCAGGAGAAAGCGCCTGAAACTGACGACTCTTTTTCAGATGTGGACTGCCATTCAAACCAG ,FFFFF,F,FFFFFFFFFFFF:F,F:F::F,FFFFFFFFFFFFFFFFFFFFFFF,F:FFF,:FFFFFFFFFF,FFF:FFFFF,FF,F:FFFFFF:F,FFFF:,::,,FFFFF:FFFF::F,FFF,:,,F:,FF,F,FF,FFF,FFFF,FF, MD:Z:41G2T7A98 RG:Z:INV_4SMALL_Aug_17_2017_1 NM:i:3 AS:i:2957
A00223:8:H7YG3DMXX:1:1101:15338:10113 16 chr7 6026731 4 151M * 0 0 CTGGTTTGAATGGCAGTCCACATCTGAAAAAGAGTCGTCAGTTTCAGGCGCTTTCTCCTGAGAGTCCACATGTTCCTGCGAGCCCCTGTCCCCTGGGGAGCTGGCCGCATACTCGCTGCTGCAGTGACTGCCCGTGTCTGGGATGCTGAAC ,FF,FFFF,FFF,FF,F,FF,:F,,:,FFF,F::FFFF:FFFFF,,::,:FFFF,F:FFFFFF:F,FF,FFFFF:FFF,FFFFFFFFFF:,FFF:F,FFFFFFFFFFFFFFFFFFFFFFF,F::F:F,F:FFFFFFFFFFFF,F,FFFFF, MD:Z:44T106 RG:Z:INV_4SMALL_Aug_17_2017_1 NM:i:1 AS:i:2999 XS:i:2957
A00223:8:H7YG3DMXX:1:1101:15881:12242 0 chr7 6026908 11 151M * 0 0 GTGCCCCGAGTCCTTCTCCACCTCCGCTCTGTCCGTAGGGTCACTGGGTCCGTGACTGGAACTCACTGCCTCTTTCTGAGATCTCAGGACGCCTTTGTCAGAGATGGCACCTGAAGTGCTAGAAGACAGCATACCCCTTTTCTGTCCTAGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFFFFFF:F,FFFFFFFFFFFFFFF:FFFFFFFFF:FF:FFF:FFFF:FFFFFFFF,FFFFFFFFF MD:Z:80G70 RG:Z:INV_4SMALL_Aug_17_2017_1 NM:i:1 AS:i:2999 XS:i:2895
A00223:8:H7YG3DMXX:1:1101:15881:12242 272 chr7 6776900 0 151M * 0 0 TCTAGGACAGAAAAGGGGTATGCTGTCTTCTAGCACTTCAGGTGCCATCTCTGACAAAGGCGTCCTGAGATCTCAGAAAGAGGCAGTGAGTTCCAGTCACGGACCCAGTGACCCTACGGACAGAGCGGAGGTGGAGAAGGACTCGGGGCAC FFFFFFFFF,FFFFFFFF:FFFF:FFF:FF:FFFFFFFFF:FFFFFFFFFFFFFFF,F:FFFFFFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MD:Z:22T0C17A28C28G50T0 RG:Z:INV_4SMALL_Aug_17_2017_1 NM:i:6 AS:i:2895
the read A00223:8:H7YG3DMXX:1:1101:1163:35383 is now fixed.