Just for the purpose of documenting, this is your shortcut to get the problem solved:
http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader Ivan On Tue, Sep 28, 2010 at 10:15 AM, Benilton Carvalho <[email protected]> wrote: > Hi Ivan, > > thanks a lot... > > This happens to 2 files I have (that's why I think the problem is with > the files)... So, the header (using samtools view -H) is concordant > with Rsamtools... > > @SQ SN:chr10 LN:135374737 > @SQ SN:chr11 LN:0 > @SQ SN:chr12 LN:0 > @SQ SN:chr13 LN:0 > @SQ SN:chr14 LN:0 > @SQ SN:chr15 LN:0 > @SQ SN:chr16 LN:0 > @SQ SN:chr17 LN:0 > @SQ SN:chr18 LN:0 > @SQ SN:chr19 LN:0 > @SQ SN:chr1 LN:0 > @SQ SN:chr20 LN:0 > @SQ SN:chr21 LN:46944323 > @SQ SN:chr22 LN:0 > @SQ SN:chr2 LN:0 > @SQ SN:chr3 LN:0 > @SQ SN:chr4 LN:0 > @SQ SN:chr5 LN:0 > @SQ SN:chr6 LN:0 > @SQ SN:chr7 LN:0 > @SQ SN:chr8 LN:0 > @SQ SN:chr9 LN:0 > @SQ SN:chrM LN:0 > @SQ SN:chrX LN:0 > @SQ SN:chrY LN:57772954 > > So, the header seems to be the culprit... > > Thank you very much, > > b > > > On 28 September 2010 15:06, Ivan Gregoretti <[email protected]> wrote: >> Hi Benilton, >> >> Does this happen with all your BAM files? >> >> Check the header in the BAM file. For mouse, it should look like this: >> >> samtools view -H myfile.bam >> @HD VN:1.0 SO:coordinate >> @SQ SN:chr1 LN:197195432 >> @SQ SN:chr2 LN:181748087 >> @SQ SN:chr3 LN:159599783 >> @SQ SN:chr4 LN:155630120 >> @SQ SN:chr5 LN:152537259 >> @SQ SN:chr6 LN:149517037 >> @SQ SN:chr7 LN:152524553 >> @SQ SN:chr8 LN:131738871 >> @SQ SN:chr9 LN:124076172 >> @SQ SN:chr10 LN:129993255 >> @SQ SN:chr11 LN:121843856 >> @SQ SN:chr12 LN:121257530 >> @SQ SN:chr13 LN:120284312 >> @SQ SN:chr14 LN:125194864 >> @SQ SN:chr15 LN:103494974 >> @SQ SN:chr16 LN:98319150 >> @SQ SN:chr17 LN:95272651 >> @SQ SN:chr18 LN:90772031 >> @SQ SN:chr19 LN:61342430 >> @SQ SN:chrX LN:166650296 >> @SQ SN:chrY LN:15902555 >> @SQ SN:chrM LN:16299 >> @SQ SN:chr13_random LN:400311 >> @SQ SN:chr16_random LN:3994 >> @SQ SN:chr17_random LN:628739 >> @SQ SN:chr1_random LN:1231697 >> @SQ SN:chr3_random LN:41899 >> @SQ SN:chr4_random LN:160594 >> @SQ SN:chr5_random LN:357350 >> @SQ SN:chr7_random LN:362490 >> @SQ SN:chr8_random LN:849593 >> @SQ SN:chr9_random LN:449403 >> @SQ SN:chrUn_random LN:5900358 >> @SQ SN:chrX_random LN:1785075 >> @SQ SN:chrY_random LN:58682461 >> >> I suspect that you have a corrupt header. >> >> Ivan >> >> >> >> >> >> On Tue, Sep 28, 2010 at 9:28 AM, Benilton Carvalho >> <[email protected]> wrote: >>> Hi, >>> >>> I wonder if you guys could help me out understanding what the problem >>> may be when reading in some BAM files I have... >>> >>> When viewing them with samtools, I get reads on chr6 (samtools view >>> file.bam chr6) >>> >>> When using scanBam/scanBamHeader, I do not get any reads on chr6 >>> (latest RSamtools on 2.11.1, but same happens with the latest devel >>> too). >>> >>> Suggestions on how to proceed in order to understand what may be going >>> on (or what I may be missing)? My guess is that the files are >>> corrupted, nothing strange comes up when using samtools... >>> >>> Thank you, >>> >>> benilton >>> >>> _______________________________________________ >>> Bioc-sig-sequencing mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >>> >> > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
