pd3
commented
2 years ago What version of bcftools are you using?
What is the output of htsfile Filt1_Adj_DP.vcf.gz? It should say something like VCF version 4.2 BGZF-compressed variant calling data. Try to use bcftools index for the indexing step instead of tabix. If none of this helps, a small test file will be required to reproduce the problem.
Note you will not gain much with --threads 28, threading is used only for the compression and decompression step.
desmodus1984
Hi,
I am studying a population and I genotyped 17 individuals. Since one of them is the reference, so has more data, I decided to separate the reference gvcf from the others, and do a first read depth filtering separately, since the reference ind has 60X while the others have ~11X, hence, I want to follow the min 1/2-averDP - max 2x-averDP, and with altogether, the reference affects the magnitude of the min/max DP. So, I separated them with GATK SelectVariants, and then merged then with Bcftools merge:
bcftools merge --threads 28 PA_113_DP.vcf.gz No_Pa90-16_DP.vcf.gz -Oz -o Adj_DP.vcf.gzTo try to verify that it worked well, I used Vcftools to check for depthvcftools --gzvcf Adj_DP.vcf.gz --depthand it worked well.No, I want to try to filter with
and first I got the error: "Failed to open Adj_DP.vcf.gz: could not load index" So I indexed it
tabix -p vcf Adj_DP.vcf.gzand now, every time I try running the filter on the Adj_DP.vcf.gz it gets me weird unreadable log file " ‹ ÿ BC Aí[Isܸ’>Ë¿a Ú=#”îÔ³zBmI¶Þh—lGÌE"³ªÐ& %•ãýø €ÅÚHÛzP¼[_ì–/ ‰dâÍ› +a"dEõÁç÷'áÈõæÍÉéÙÝñÍÁ»Ó£ƒ«ÃÛÛÝ#P¹dµf‚ ¼>,K4a¥©PM•‚âõ ¯Þ¼9<»³../îoŽO6çÜ@-A× Q>GµPŠK@ÔÀpªÙƒù]‚iÒHϘB¥È©™lÁ×:× -7ñÏÄ#úÖÐ’éy;þòæü°åçðh÷¢©Æ nvïæ5 œr S=¡ d9 Ö3…&B"=$a‚(/ Ÿ þbÜv Y€D%Sz¡€5šGW Mò3šu-Å«¨6„hÑGoÍo… ™ž¡óë?ŠíŸcZ 3!a±Pü¾MþÃõsÈ .ô¼t=¬¸w[(·Z2> Ùž|~zqÿ<-œ3Ϊ¦BGWHŒÈ(¬° 5øüþK‘Ý&qõ,¯fsÅrZ¢zFãS4£uÙÊÍx»ñ™à»¨°“Æv„x´¤»Í Ë¥7Z78P˜] ¡´“‘Hp@” =ÙãóôÈ…ÏÓ£M g Íg¨áì[fÄBQMÙp¤hU—€ÞŽ¸ÐˆæR(µhV¿£\p¹VHB.äb“Ùù Õ©MÝ“à¬àÃOòÂðZ²ïP좫™„«œ–P ’}…’Í„(ZÚ.öŒBT¡&Œ·ú4:7«jÈÙ„›ÿ/·ÏÙTW qhôVÏk£Ùrn)ÔB1»jbbÿž0©4z ’Q®;6èžUÝ<Ϭ>ñ\ðÂ’ ¥q ç°”Ú,„¦mÏE…Q„Y EçÆ&Þ•bJ<T¿]Í¥e‰˜BRðiÃÛ?;ßé$^l”\TµàÀ5Ršj¦4Ëzœ±|f»$SÕqÂÔ äo ?Ñ\£;PÚlú4äf®4>r̨Y–> Þýï{QU”gŒƒåí½¨ÆŒƒ1gµ»Þùz½a,]7ÚÐ7£éè!ŸŒ¦ßÆÝ} úmúýÆÓ‹``èÕ!!þ³— I½ÁÁ~Ôo>< Ó~ëùE4ÔH切ˆeƒ„ r– ¶†dˆÝÔ jÍÖÆ®öu5W€g´ÓÑ„*Mƹà 5Ö©\S&±%ÊÆZÞ„– Æc ô+ S^(L5®šR3㨰˜ aÌxÝhÌVÂxÁ|9±¢îq{ 2>Å”s¡×PË¡ÆbðÊãtÍlÊ…„N8…•¦R ÑhÅ ÀŒk´\µr5¥`JS£ÃjEŸVIs there a reason, Vcftools can generate a reasonable coherent depth analysis, while Bcftools fails? Previously, that same code for filtering worked but not I do not understand that weird log file.
Best;