I have difficulty understanding the statistics generated by PiCard BamIndexStats, part of the my stats results is:
chr7_gl000195_random length= 182896 Aligned= 3135 Unaligned= 0 chr8 length= 146364022 Aligned= 1627297 Unaligned= 0 chr8_gl000196_random length= 38914 Aligned= 869 Unaligned= 0
Does this result mean that, for chr 7 and 8, 100% of the reads are aligned to the chromosomes regions? I used bwa mem to do the alignment, is it sort of too good to be true?
•
written
by
newDNASeqer
1 answer
You may have bam file and corresponding index files for that cases here !! So as I think It will always show 100% Match here !! I may be wrong but would like to see other response !! Meanwhile what about other Chromosomes also !!
Log in to answer this question.
-
undefined chro name in vcf header
written by Mahdi&Christ •
-
Bwa And Bwa Mem Produce Different Alignments
written by Rad
-
How To Get The Correct Alignment Statistics After Using Bwa Mem With -M Option
written by skm770 •
-
Bowtie Outputs Hits That Are Shorter Than The Reads Aligned
written by Click downvote
-
How To Retrieve Chromosome Lengths Using Bsgenome Package?
written by James Ashmore •
-
Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
written by newDNASeqer
-
Paired-End Reads Alignment For Variant Calling ?
written by newDNASeqer
-
Can You Make A Bam File Picard Compatible? I Forgot -M With Bwa Mem
written by ajc8 •
-
Why Pair Ends Data'S Ecah Pair'S Alignment Statistic And The Sum Of Them Are Different
written by litiancheng.gansu •
-
Htseq Count Finding No Feature
written by joaslucas •
Did you run with the LENIENT flag? I ask because Picard will discard unmapped reads if they have a MAPQ of zero.
Other things that would be helpful: can you tell us your command line for Picard, and perhaps include a few lines from the BAM?