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Old 06-13-2019, 09:50 AM   #227
bwubb
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Location: Philadelphia

Join Date: Jan 2012
Posts: 58
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Quote:
Originally Posted by GenoMax View Post
Have you tried adding "VALIDATION_STRINGENCY=LENIENT" to your picard command? Default value is STRICT and sometime it leads to picard throwing errors like this.
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Yes indeed, but it will still be an ERROR.

However, after more tinkering I was able to come up with a combination that worked.

Code:
reformat.sh -Xmx5g in=qSortA.bam out=qSortA_reads.fq
reformat.sh -Xmx5g int=t addcolon=t uniquenames=t in=qSortA_reads.fq out=out_reads.fq
repair.sh -Xmx5g in=out_reads.fq out1=reads1.fq out2=reads2.fq
Taking those reads into alignment and so forth will pass ValidateSamFile. Im guessing these actions are allowing me to completely rewrite the pairing status, which I am perfectly ok with.

Thank you for the comments and help!
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