I think that some FASTQ files containing exome reads from the European trio in the 1KGP project are missing.
Read groups in an exome file (NA12878.chrom22.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam):
If you take a look at the FASTQ raw reads, you will find all read groups but SRR013620 for NA12878. For NA12891, the read group SRR013888 is missing; and for NA12892, SRR013619. The African trio (NA19238-40) is OK.
But the reads in read group SRR013620 are present in the BAM file:
After searching on Google, I found the read group SRR013620 at an EBI site.
The files at the 1KGP FTP site are filtered ("filt" in the file names). Those at the EBI site do not have that substring suggesting that they are unfiltered. A comparison of the files SRR013890.filt.fastq.gz and SRR013890/SRR013890.fastq.gz shows that the 1KGP is smaller (294 MB vs 303 MB), confirming the hypothesis.
I found in another thread the sequence index file of 1KGP that the md5sum is missing (described here), suggesting that the missing FASTQ files are not supposed to exist.
Can anybody tell me what is going on here? Are some FASTQ files missing, or located somewhere else? Can I use the FASTQ files at the EBI site, and do they have lower quality if unfiltered?
Read groups in an exome file (NA12878.chrom22.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam):
Code:
daggy@daggy-Studio-XPS-8100:~/Downloads$ samtools view -H NA12878/exon/NA12878.chrom22.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam ... @RG ID:SRR013620 PL:ILLUMINA LB:Solexa-5324 PI:0 DS:SRP000033 SM:NA12878 CN:BI @RG ID:SRR013890 PL:ILLUMINA LB:Solexa-7288 PI:0 DS:SRP000033 SM:NA12878 CN:BI @RG ID:SRR014820 PL:ILLUMINA LB:Solexa-10292 PI:300 DS:SRP000033 SM:NA12878 CN:BI @RG ID:SRR015370 PL:ILLUMINA LB:2773962043 PI:0 DS:SRP000033 SM:NA12878 CN:WUGSC @RG ID:SRR016607 PL:ILLUMINA LB:Solexa-11435 PI:201 DS:SRP000033 SM:NA12878 CN:BI @RG ID:SRR017279 PL:ILLUMINA LB:Solexa-7288 PI:0 DS:SRP000033 SM:NA12878 CN:BI
But the reads in read group SRR013620 are present in the BAM file:
Code:
daggy@daggy-Studio-XPS-8100:~/Downloads$ samtools view NA12878.chrom22.ILLUMINA.bwa.CEU.exon_targetted.20100311.bam | grep SRR013620 | wc 142742 3118113 41310387
The files at the 1KGP FTP site are filtered ("filt" in the file names). Those at the EBI site do not have that substring suggesting that they are unfiltered. A comparison of the files SRR013890.filt.fastq.gz and SRR013890/SRR013890.fastq.gz shows that the 1KGP is smaller (294 MB vs 303 MB), confirming the hypothesis.
I found in another thread the sequence index file of 1KGP that the md5sum is missing (described here), suggesting that the missing FASTQ files are not supposed to exist.
Can anybody tell me what is going on here? Are some FASTQ files missing, or located somewhere else? Can I use the FASTQ files at the EBI site, and do they have lower quality if unfiltered?